From f4a55ef45fa0ffa17e75231656e47b1a3bb3ff52 Mon Sep 17 00:00:00 2001 From: Alex Bigelow Date: Sat, 23 Mar 2024 15:41:47 -0700 Subject: [PATCH] Lots of fixes, updates --- build.js | 7 + cv.html | 158 +- cv/experience/reviewing.md | 10 +- cv/experience/stardog.md | 10 +- .../papers/2022_traveler/citation.bib | 13 +- .../papers/2022_traveler/publication.url | 1 + .../papers/2023_chi_elephants/abstract.txt | 1 + .../papers/2023_chi_elephants/citation.bib | 17 + .../papers/2023_chi_elephants/publication.url | 1 + funding.html | 16 +- sitemap.xml | 56 +- styles/fundingStyles.less | 3 + views/CvView/CvView.js | 49 +- views/CvView/buildGraph.js | 0 views/CvView/data.json | 3312 +++++++++-------- views/CvView/mapping.sms | 32 +- views/CvView/model.ttl | 10 +- views/CvView/style.less | 79 +- views/MenuView/MenuView.js | 8 +- views/MenuView/default.json | 3 +- 20 files changed, 2097 insertions(+), 1689 deletions(-) create mode 100644 cv/publications/papers/2022_traveler/publication.url create mode 100644 cv/publications/papers/2023_chi_elephants/abstract.txt create mode 100644 cv/publications/papers/2023_chi_elephants/citation.bib create mode 100644 cv/publications/papers/2023_chi_elephants/publication.url create mode 100644 views/CvView/buildGraph.js diff --git a/build.js b/build.js index 35d68f4..310706d 100755 --- a/build.js +++ b/build.js @@ -40,13 +40,20 @@ const PARSERS = { author = author.split(/[\s,]+/); return author.slice(1).join(' ') + ' ' + author[0]; }); + result.authorLastNames = result.author.split(/\s+and\s+/).map((author) => { + author = author.split(/[\s,]+/); + return author[0]; + }); if (result.authorList.length > 2) { result.joinedAuthorList = result.authorList.slice(0, -1).join(', ') + ', and ' + result.authorList[result.authorList.length - 1]; + result.shortAuthorList = result.authorLastNames.slice(0, -1).join(', ') + + ', and ' + result.authorLastNames[result.authorLastNames.length - 1]; } else { result.joinedAuthorList = result.authorList.join(' and '); + result.shortAuthorList = result.authorLastNames.join(' and '); } // Fake 'howpublished' field for theses and patents diff --git a/cv.html b/cv.html index 02cceec..2fc4105 100644 --- a/cv.html +++ b/cv.html @@ -1,86 +1,94 @@ - - - - - - - - - - -
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Alex Bigelow

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Experience

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Employment
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+ Selected + Publications +

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Alex Bigelow

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Education

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PhD Computing: Data Management and Analysis
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2019
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  • University of Utah, Salt Lake City, UT
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  • Advisor: Dr. Miriah Meyer
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Education

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PhD Computing: Data Management and Analysis
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2019
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  • University of Utah, Salt Lake City, UT
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  • Advisor: Dr. Miriah Meyer
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B.S. Computer Science
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2012
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  • University of Utah, Salt Lake City, UT
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B.S. Computer Science
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2012
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  • University of Utah, Salt Lake City, UT
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Experience

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Employment
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- Selected - Publications -

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Theses
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Preprints
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Refereed Conference and Journal Papers
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Patents
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Extended Abstracts
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Posters
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printHelper

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printHelper

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click roles or publication titles for more details
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printHelper

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printHelper

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+ diff --git a/cv/experience/reviewing.md b/cv/experience/reviewing.md index 15e91de..1eedb1f 100644 --- a/cv/experience/reviewing.md +++ b/cv/experience/reviewing.md @@ -1,14 +1,12 @@ --- title: Peer Reviewer start: 2015 -stop: Present +stop: 2024 service: true meta: - - IEEE Information Visualization (2016-2021), Short Papers Program Committee (2020) - - Eurovis VGTC Conference on Visualization (2016, 2020, 2021) - - IEEE Conference on Visual Analytics Science and Technology (VAST) (2017, 2019-2021) - - ACM CHI Conference on Human Factors in Computing Systems (2015, 2017-2020) - - IEEE Transactions on Visualization and Computer Graphics (2019-2021) + - IEEE VIS Conference, IEEE Transactions on Visualization and Computer Graphics (2016–2023), Short Papers Program Committee (2020) + - Eurovis VGTC Conference on Visualization (2016, 2020–2022) + - ACM CHI Conference on Human Factors in Computing Systems (2015, 2017–2022, 2024) - Workshop on Visualization in Practice (2017) - alt.VIS Workshop (2021) --- diff --git a/cv/experience/stardog.md b/cv/experience/stardog.md index 2b6700e..f0ffd97 100644 --- a/cv/experience/stardog.md +++ b/cv/experience/stardog.md @@ -1,11 +1,17 @@ --- title: Software Engineer start: 2021 -stop: Present +stop: 2024 meta: - Stardog Union - Arlington, VA reference: 'Mentors: Annee Barrett, Dr. Jason Rogers, Laura Firey Monroe, Dr. Michael Grove, Paul Ambro' --- -Since starting at Stardog, I've helped mock up, implement, and deploy a visual network modeling tool, as well as contribute to the development of an existing IDE and network visualization tool. +At Stardog, I helped design, implement ship, and maintain several user-facing applications (and associated libraries and Cloud UI), used by all of Stardog's customers and beyond. These included: + +- Stardog Designer, a graph modeling and mapping tool which was largely based off my Origraph research work +- Stardog Explorer, a simple node-link diagram visualization tool with an accessible (yet very expressive) visual query building interface +- Stardog Studio, an IDE for writing and editing queries, and managing Stardog databases and virtual graphs + +I was also heavily involved in the design and integration of Stardog Voicebox—a Large Language Model-powered chat assistant that translated natural language into SPARQL queries, executed the queries against data in Stardog, and summarized the results with an explainable UX with citations and a visual rendering of the query, that communicated exactly how the AI was able to find its answers. diff --git a/cv/publications/papers/2022_traveler/citation.bib b/cv/publications/papers/2022_traveler/citation.bib index 1a9c4e5..865059f 100644 --- a/cv/publications/papers/2022_traveler/citation.bib +++ b/cv/publications/papers/2022_traveler/citation.bib @@ -1,6 +1,11 @@ @article{sakin2022traveler, - title={Traveler: Navigating Task Parallel Traces for Performance Analysis}, - author={Sakin, Sayef Azad and Bigelow, Alex and Tohid, R and Scully-Allison, Connor and Scheidegger, Carlos and Brandt, Steven R. and Taylor, Christopher and Huck, Kevin A. and Kaiser, Hartmut and Isaacs, Katherine E.}, - journal={arXiv preprint arXiv:2208.00109}, - year={2022} + author={Sakin, Sayef Azad and Bigelow, Alex and Tohid, R. and Scully-Allison, Connor and Scheidegger, Carlos and Brandt, Steven R. and Taylor, Christopher and Huck, Kevin A. and Kaiser, Hartmut and Isaacs, Katherine E.}, + journal={IEEE Transactions on Visualization and Computer Graphics}, + title={Traveler: Navigating Task Parallel Traces for Performance Analysis}, + year={2023}, + volume={29}, + number={1}, + pages={788-797}, + keywords={Task analysis;Performance analysis;Measurement;Data visualization;Codes;Navigation;High performance computing;software visualization;parallel computing;traces;performance analysis;event sequence visualization}, + doi={10.1109/TVCG.2022.3209375} } \ No newline at end of file diff --git a/cv/publications/papers/2022_traveler/publication.url b/cv/publications/papers/2022_traveler/publication.url new file mode 100644 index 0000000..7e1c6f1 --- /dev/null +++ b/cv/publications/papers/2022_traveler/publication.url @@ -0,0 +1 @@ +https://doi.org/10.1109/TVCG.2022.3209375 \ No newline at end of file diff --git a/cv/publications/papers/2023_chi_elephants/abstract.txt b/cv/publications/papers/2023_chi_elephants/abstract.txt new file mode 100644 index 0000000..cecd64c --- /dev/null +++ b/cv/publications/papers/2023_chi_elephants/abstract.txt @@ -0,0 +1 @@ +Two people looking at the same dataset will create different mental models, prioritize different attributes, and connect with different visualizations. We seek to understand the space of data abstractions associated with mental models and how well people communicate their mental models when sketching. Data abstractions have a profound influence on the visualization design, yet it’s unclear how universal they may be when not initially influenced by a representation. We conducted a study about how people create their mental models from a dataset. Rather than presenting tabular data, we presented each participant with one of three datasets in paragraph form, to avoid biasing the data abstraction and mental model. We observed various mental models, data abstractions, and depictions from the same dataset, and how these concepts are influenced by communication and purpose-seeking. Our results have implications for visualization design, especially during the discovery and data collection phase. \ No newline at end of file diff --git a/cv/publications/papers/2023_chi_elephants/citation.bib b/cv/publications/papers/2023_chi_elephants/citation.bib new file mode 100644 index 0000000..1af46a4 --- /dev/null +++ b/cv/publications/papers/2023_chi_elephants/citation.bib @@ -0,0 +1,17 @@ +@inproceedings{williams2023elephants, +author = {Williams, Katy and Bigelow, Alex and Isaacs, Katherine E.}, +title = {Data Abstraction Elephants: The Initial Diversity of Data Representations and Mental Models}, +year = {2023}, +isbn = {9781450394215}, +publisher = {Association for Computing Machinery}, +address = {New York, NY, USA}, +url = {https://doi.org/10.1145/3544548.3580669}, +doi = {10.1145/3544548.3580669}, +abstract = {Two people looking at the same dataset will create different mental models, prioritize different attributes, and connect with different visualizations. We seek to understand the space of data abstractions associated with mental models and how well people communicate their mental models when sketching. Data abstractions have a profound influence on the visualization design, yet it’s unclear how universal they may be when not initially influenced by a representation. We conducted a study about how people create their mental models from a dataset. Rather than presenting tabular data, we presented each participant with one of three datasets in paragraph form, to avoid biasing the data abstraction and mental model. We observed various mental models, data abstractions, and depictions from the same dataset, and how these concepts are influenced by communication and purpose-seeking. Our results have implications for visualization design, especially during the discovery and data collection phase.}, +booktitle = {Proceedings of the 2023 CHI Conference on Human Factors in Computing Systems}, +articleno = {803}, +numpages = {24}, +keywords = {Human-centered computing, data abstractions, visualization theory}, +location = {, Hamburg, Germany, }, +series = {CHI '23} +} \ No newline at end of file diff --git a/cv/publications/papers/2023_chi_elephants/publication.url b/cv/publications/papers/2023_chi_elephants/publication.url new file mode 100644 index 0000000..906a179 --- /dev/null +++ b/cv/publications/papers/2023_chi_elephants/publication.url @@ -0,0 +1 @@ +https://doi.org/10.1145/3544548.3580669 \ No newline at end of file diff --git a/funding.html b/funding.html index 3d9a844..7963b4f 100755 --- a/funding.html +++ b/funding.html @@ -17,22 +17,18 @@
-

Consulting

+

Hire Me!

+

+ I am currently on the job market—if you need to consult a data + visualization expert or if you have an employment opportunity that you + think might be a good fit, please contact me! +

If you need informal (free) expert advice about anything on this page, I try to attend Arizona Research Bazaar events as often as I can—come grab a Hacky Hour beer, and let's chat!

-

- If you need help strategizing about data (especially if you're trying to - figure out how to interpret existing data sources as a graph), check out - the offerings at - Stardog, or - feel free to - contact me - directly. -

diff --git a/sitemap.xml b/sitemap.xml index 9bc2dc1..50aaee9 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -1,59 +1,59 @@ - 2012-05-10 - https://alex-r-bigelow.github.io/blog/Installing_pycairo_or_py2cairo_on_OS_X_Lion/index.html - - - 2013-11-13 - https://alex-r-bigelow.github.io/blog/Brython_and_Knockout/index.html + 2012-01-19 + https://alex-r-bigelow.github.io/blog/Macfusion_MacFUSE_Lion/index.html - 2012-01-18 - https://alex-r-bigelow.github.io/blog/Getting_PHP_to_run_in_OS_X_Lion/index.html + 2013-04-19 + https://alex-r-bigelow.github.io/blog/Exporting_video_from_Tableau/index.html - 2013-06-10 - https://alex-r-bigelow.github.io/blog/epstopdf_on_OS_X/index.html + 2016-03-12 + https://alex-r-bigelow.github.io/blog/LG_e980_Flashing_Guide/index.html - 2012-05-15 - https://alex-r-bigelow.github.io/blog/PySide_in_Eclipse/index.html + 2012-03-26 + https://alex-r-bigelow.github.io/blog/webpy_and_Sessions/index.html - 2013-08-14 - https://alex-r-bigelow.github.io/blog/Toshiba_Portege_M200_Linux/index.html + 2012-05-10 + https://alex-r-bigelow.github.io/blog/Installing_pycairo_or_py2cairo_on_OS_X_Lion/index.html - 2013-11-14 - https://alex-r-bigelow.github.io/blog/MacFusion_OSXFUSE_and_Mavericks/index.html + 2013-03-29 + https://alex-r-bigelow.github.io/blog/Efficiently_running_a_SimpleHTTPServer_from_Eclipse/index.html - 2012-10-23 - https://alex-r-bigelow.github.io/blog/Adding_to_XCode_Menu/index.html + 2012-05-15 + https://alex-r-bigelow.github.io/blog/PySide_in_Eclipse/index.html - 2013-04-19 - https://alex-r-bigelow.github.io/blog/Exporting_video_from_Tableau/index.html + 2013-06-10 + https://alex-r-bigelow.github.io/blog/epstopdf_on_OS_X/index.html - 2013-03-29 - https://alex-r-bigelow.github.io/blog/Efficiently_running_a_SimpleHTTPServer_from_Eclipse/index.html + 2013-11-14 + https://alex-r-bigelow.github.io/blog/MacFusion_OSXFUSE_and_Mavericks/index.html - 2016-03-12 - https://alex-r-bigelow.github.io/blog/LG_e980_Flashing_Guide/index.html + 2013-11-13 + https://alex-r-bigelow.github.io/blog/Brython_and_Knockout/index.html 2015-07-06 https://alex-r-bigelow.github.io/blog/Graph_Databases/index.html - 2012-03-26 - https://alex-r-bigelow.github.io/blog/webpy_and_Sessions/index.html + 2013-08-14 + https://alex-r-bigelow.github.io/blog/Toshiba_Portege_M200_Linux/index.html - 2012-01-19 - https://alex-r-bigelow.github.io/blog/Macfusion_MacFUSE_Lion/index.html + 2012-10-23 + https://alex-r-bigelow.github.io/blog/Adding_to_XCode_Menu/index.html + + + 2012-01-18 + https://alex-r-bigelow.github.io/blog/Getting_PHP_to_run_in_OS_X_Lion/index.html 2020-11-27 diff --git a/styles/fundingStyles.less b/styles/fundingStyles.less index 42b9f52..057fd44 100644 --- a/styles/fundingStyles.less +++ b/styles/fundingStyles.less @@ -60,6 +60,8 @@ h3 img { display: flex; flex-wrap: wrap; justify-content: space-around; + margin-bottom: 2rem; + &.reverse { flex-direction: row-reverse; justify-content: flex-end; @@ -73,6 +75,7 @@ h3 img { } @media (min-width: 1078px) { .splitscreen { + min-height: 30em; .anchor { max-width: 420px; } diff --git a/views/CvView/CvView.js b/views/CvView/CvView.js index 754f9e3..c3d61ee 100644 --- a/views/CvView/CvView.js +++ b/views/CvView/CvView.js @@ -9,7 +9,7 @@ class CvView extends uki.View { ]); super(options); - window.addEventListener('beforeprint', () => { + window.addEventListener('beforeprint', async () => { // Programmatically add contact info to a printed version of the CV... // really lame version of obfuscation, but this should stop *most* evil // spammers @@ -31,8 +31,10 @@ class CvView extends uki.View { }); window.enableFullPrint = () => { + window.fullPrintEnabled = true; d3.selectAll('.showInFullPrint').classed('hideInPrint', false); d3.selectAll('.hideInFullPrint').classed('showInPrint', false); + this.render(); }; } @@ -40,8 +42,8 @@ class CvView extends uki.View { return this.getNamedResource('data'); } - async setup () { - await super.setup(...arguments); + async draw () { + await super.draw(...arguments); for (const pubChunk of this.d3el.selectAll('.pubchunk').nodes()) { const pubType = pubChunk.dataset.type; @@ -96,10 +98,14 @@ class CvView extends uki.View { } }); - pubsEnter.append('ul').classed('meta', true) + pubsEnter.append('ul').classed('meta', true); + + let meta = pubs.select('.meta') .selectAll('li') - .data(d => this.getPubMetaFields(d)).enter().append('li') - .attr('class', d => d.fieldname) + .data(d => this.getPubMetaFields(d)); + const metaEnter = meta.enter().append('li') + .attr('class', d => d.fieldname); + meta = meta.merge(metaEnter) .text(d => d.fieldvalue); } @@ -111,16 +117,22 @@ class CvView extends uki.View { ].map(fieldnames => { for (const fieldname of fieldnames) { const bib = pub['citation.bib'].contents; - let fieldvalue = bib[fieldname] || - (pub['meta.json'] && pub['meta.json'].contents[fieldname]); + const metadata = bib[fieldname] ? bib : pub['meta.json']?.contents || {}; + let fieldvalue = metadata[fieldname]; if (fieldvalue) { - // Add extra info for some fields: + // Add / change extra info for some fields: if (fieldname === 'journal' && bib.volume && bib.pages) { fieldvalue += ` ${bib.volume}:${bib.pages}`; } if (fieldname === 'booktitle' && bib.pages) { fieldvalue += ` pp. ${bib.pages}`; } + if (!window.fullPrintEnabled && + fieldname === 'joinedAuthorList' && + metadata.authorList?.length > 6 && + metadata.shortAuthorList) { + fieldvalue = metadata.shortAuthorList; + } return { fieldname, fieldvalue }; } } @@ -252,8 +264,9 @@ class CvView extends uki.View { return bTemp - aTemp; }); - const entriesEnter = container.selectAll('.entry') - .data(entriesList).enter().append('div').classed('entry', true) + let entries = container.selectAll('.entry') + .data(entriesList); + const entriesEnter = entries.enter().append('div').classed('entry', true) .classed('hideInPrint showInFullPrint', d => d?.contents?.data?.hideInPrint); entriesEnter.append('h6') .classed('title', true) @@ -261,13 +274,14 @@ class CvView extends uki.View { entriesEnter.append('h6') .classed('date', true) .html(d => this.formatExpTimestamp(d)); + entries = entries.merge(entriesEnter); const metaFields = [ ['meta'], ['reference'] ]; entriesEnter.append('ul').classed('meta', true); - const metaEnter = entriesEnter.select('.meta').selectAll('li') + let meta = entries.select('.meta').selectAll('li') .data(d => metaFields.map(fieldnames => { for (const fieldname of fieldnames) { const fieldvalue = d.contents.data[fieldname]; @@ -276,11 +290,16 @@ class CvView extends uki.View { } } return null; - }).filter(d => d !== null)).enter().append('li'); - metaEnter.attr('class', d => d.fieldname) + }).filter(d => d !== null)); + const metaEnter = meta.enter().append('li'); + metaEnter.attr('class', d => d.fieldname); + meta = meta.merge(metaEnter) .html(d => { if (d.fieldvalue instanceof Array) { - return d.fieldvalue.join('
'); + const breakTag = window.fullPrintEnabled + ? '
' + : ', 
'; + return d.fieldvalue.join(breakTag); } else { return d.fieldvalue; } diff --git a/views/CvView/buildGraph.js b/views/CvView/buildGraph.js new file mode 100644 index 0000000..e69de29 diff --git a/views/CvView/data.json b/views/CvView/data.json index e675399..7502c8a 100644 --- a/views/CvView/data.json +++ b/views/CvView/data.json @@ -1,2135 +1,2433 @@ { - "experience": { - "ta_2.md": { - "url": "/cv/experience/ta_2.md", - "path": [ - "experience" - ], - "name": "ta_2", - "extension": "md", - "contents": { - "content": "", - "data": { - "title": "Teaching Assistant", - "season": "Fall", - "year": 2015, - "meta": [ - "CS 5630 / 6630 Visualization", - "University of Utah, Salt Lake City, UT" + "publications": { + "theses": { + "2019_phd_dissertation": { + "abstract.txt": { + "url": "/cv/publications/theses/2019_phd_dissertation/abstract.txt", + "path": [ + "publications", + "theses", + "2019_phd_dissertation" ], - "reference": "with Dr. Alexander Lex, using D3.js", - "links": { - "Course page": "http://dataviscourse.net/2015/" + "name": "abstract", + "extension": "txt", + "contents": "Iteration is a ubiquitous need across many different visualization design workflows. For visual design, practitioners often need to transition between the automated generation of visuals and manual drawing; however, existing software makes free-form iteration between these modalities difficult or impossible. A similar challenge exists for data as well: data abstractions often need to be adjusted; however, many data reshaping operations— particularly graph wrangling operations—have support only in programming environments that may not be accessible to many visualization designers.\n\nThis dissertation begins with an effort to better understand how graphic designers, a specific subset of the broader visualization community, work with data. The lessons from that effort inspire our remaining contributions, which are directed toward the broader community of visualization practitioners: first, we present a software model and a system that make it possible to iterate between drawing and generative visualization. Second, we present a visual technique that enables inquiry into the relationship between two specific graph data wrangling operations: pivoting and filtering. Finally, we present an interface that supports a broader range of graph data wrangling operations that enable iteration between many different graph data abstractions.\n", + "filename": "abstract.txt", + "lastmod": "2020-09-27" + }, + "citation.bib": { + "url": "/cv/publications/theses/2019_phd_dissertation/citation.bib", + "path": [ + "publications", + "theses", + "2019_phd_dissertation" + ], + "name": "citation", + "extension": "bib", + "contents": { + "title": "Reflections, Models, and Software for Iterative Visualization Design", + "author": "Bigelow, Alex", + "school": "University of Utah", + "year": "2019", + "authorList": [ + "Alex Bigelow" + ], + "authorLastNames": [ + "Bigelow" + ], + "joinedAuthorList": "Alex Bigelow", + "shortAuthorList": "Bigelow", + "howpublished": "University of Utah PhD Dissertation" }, - "referenceList": [ - "Alexander Lex" - ] + "filename": "citation.bib", + "lastmod": "2020-09-27" }, - "isEmpty": false, - "excerpt": "" + "publication.pdf": { + "url": "/cv/publications/theses/2019_phd_dissertation/publication.pdf", + "path": [ + "publications", + "theses", + "2019_phd_dissertation" + ], + "name": "publication", + "extension": "pdf", + "filename": "publication.pdf", + "lastmod": "2020-09-27" + } }, - "filename": "ta_2.md", - "lastmod": "2020-12-04" - }, - "resbaz.md": { - "url": "/cv/experience/resbaz.md", - "path": [ - "experience" - ], - "name": "resbaz", - "extension": "md", - "contents": { - "content": "

I benefitted from, and endeavored to assist with, a University of Arizona campus outreach group that provided regular meetups for people on campus and members of the community to help each other with applied programming or data challenges.

\n

We also organized a free weeklong series of workshops that provided training in a variety of data science topics.

", - "data": { - "title": "Steering Committee Member", - "start": 2019, - "stop": "Present", - "service": true, - "meta": [ - "Arizona Research Bazaar Steering Committee", - "University of Arizona, Tucson, AZ" - ] + "2012_bs_thesis": { + "abstract.txt": { + "url": "/cv/publications/theses/2012_bs_thesis/abstract.txt", + "path": [ + "publications", + "theses", + "2012_bs_thesis" + ], + "name": "abstract", + "extension": "txt", + "contents": "Some misunderstanding is inevitable in any interdisciplinary work, and recognizing and handling misunderstanding quickly is vital to the success of a collaboration. Many misunderstandings arise from what appears to be common knowledge to a domain scientist, but is not something that a computer scientist would think to ask about. The use of experimental visualization as an inter-collaboration communication tool can highlight these important misunderstandings that would otherwise severely impair the collaboration.\n\nVisualization itself, however, is a powerful tool; if used carefully it can open doors to understanding and discovery, but it can also control, warp, or even limit how a visualization designer (and consequently a scientist) thinks about a problem. A willingness to abandon erroneous designs and even systems, regardless of the effort involved in creating and understanding them, is also very important for such a collaboration.\n\nThis case study of data exploration via experimental visualization is in the space of next-generation sequencing data. For most of the history of genetics, the main bottleneck in the rate of discovery has been the difficulty in obtaining data. Next generation sequencing is a relatively new technology that allows biologists a way to obtain genetic data at a fraction of the cost and unprecedented speeds compared to conventional sequencing. With the advent of NGS data, the bottleneck has shifted from the burden of data acquisition to the analysis of huge amounts of data.\n", + "filename": "abstract.txt", + "lastmod": "2020-09-27" }, - "isEmpty": false, - "excerpt": "" - }, - "filename": "resbaz.md", - "lastmod": "2020-12-03" - }, - "genepi.md": { - "url": "/cv/experience/genepi.md", - "path": [ - "experience" - ], - "name": "genepi", - "extension": "md", - "contents": { - "content": "

For two years, I developed and experimented with Next-Generation Sequencing processing and analysis tools. We also worked with large pedigrees from the Utah Population Database.

\n

I gained firsthand exposure to large, messy, and heavily nuanced data. We also grappled with task ambiguity—as these were new, rich resources, they presented truly wicked problems: once we could see one pattern in the data, it made us ask questions that needed an entirely different perspective. I was also able to observe the difficulties, potential errors, and lack of standards and support that domain scientists face when trying to work with new kinds of data.

", - "data": { - "title": "Research Assistant", - "start": 2010, - "stop": 2012, - "meta": [ - "Internal Medicine", - "Division of Genetic Epidemiology", - "University of Utah, Salt Lake City, UT" + "citation.bib": { + "url": "/cv/publications/theses/2012_bs_thesis/citation.bib", + "path": [ + "publications", + "theses", + "2012_bs_thesis" ], - "reference": "Advisor: Dr. Nicola J. Camp", - "links": { - "BS Thesis": "/cv#2012_bs_thesis", - "Cancer Research Papers": [ - "/cv#2016_haplotype", - "/cv#2014_targeted" - ] + "name": "citation", + "extension": "bib", + "contents": { + "title": "Driving Genetics With Experimental Visualization", + "author": "Bigelow, Alex", + "school": "University of Utah", + "year": "2012", + "authorList": [ + "Alex Bigelow" + ], + "authorLastNames": [ + "Bigelow" + ], + "joinedAuthorList": "Alex Bigelow", + "shortAuthorList": "Bigelow", + "howpublished": "University of Utah Thesis" }, - "referenceList": [ - "Nicola J. Camp" - ] + "filename": "citation.bib", + "lastmod": "2020-09-27" }, - "isEmpty": false, - "excerpt": "" - }, - "filename": "genepi.md", - "lastmod": "2020-12-04" + "publication.pdf": { + "url": "/cv/publications/theses/2012_bs_thesis/publication.pdf", + "path": [ + "publications", + "theses", + "2012_bs_thesis" + ], + "name": "publication", + "extension": "pdf", + "filename": "publication.pdf", + "lastmod": "2020-09-27" + } + } }, - "reviewing.md": { - "url": "/cv/experience/reviewing.md", - "path": [ - "experience" - ], - "name": "reviewing", - "extension": "md", - "contents": { - "content": "", - "data": { - "title": "Peer Reviewer", - "start": 2015, - "stop": "Present", - "service": true, - "meta": [ - "IEEE Information Visualization (2016-2021), Short Papers Program Committee (2020)", - "Eurovis VGTC Conference on Visualization (2016, 2020, 2021)", - "IEEE Conference on Visual Analytics Science and Technology (VAST) (2017, 2019-2021)", - "ACM CHI Conference on Human Factors in Computing Systems (2015, 2017-2020)", - "IEEE Transactions on Visualization and Computer Graphics (2019-2021)", - "Workshop on Visualization in Practice (2017)", - "alt.VIS Workshop (2021)" - ] + "patents": { + "2017_backfilling": { + "US9569558.pdf": { + "url": "/cv/publications/patents/2017_backfilling/US9569558.pdf", + "path": [ + "publications", + "patents", + "2017_backfilling" + ], + "name": "US9569558", + "extension": "pdf", + "filename": "US9569558.pdf", + "lastmod": "2020-09-27" }, - "isEmpty": false, - "excerpt": "" - }, - "filename": "reviewing.md", - "lastmod": "2021-09-30" - }, - "sci.md": { - "url": "/cv/experience/sci.md", - "path": [ - "experience" - ], - "name": "sci", - "extension": "md", - "contents": { - "content": "

As a PhD student, I researched the effects that data can have on graphic designers as they create visualizations, how to support more iterative workflows between programming and drawing, and how to better support ideation about different network data abstractions.

", - "data": { - "title": "Research Assistant", - "start": 2013, - "stop": 2018, - "meta": [ - "School of Computing", - "Scientific Computing and Imaging (SCI) Institute", - "University of Utah, Salt Lake City, UT" + "abstract.txt": { + "url": "/cv/publications/patents/2017_backfilling/abstract.txt", + "path": [ + "publications", + "patents", + "2017_backfilling" ], - "reference": "Advisor: Dr. Miriah Meyer", - "referenceList": [ - "Miriah Meyer" - ] + "name": "abstract", + "extension": "txt", + "contents": "Disclosed herein is system for updating a graph-based data structure comprising a processor that hosts an algorithm to incrementally update underlying data and abstractions for a graph-based data structure based on popular user selections; a user interface that is in two-way operative communication with the processor; where the user interface is operative to present graph-based data structures to a user for updating; and a memory database that is in communication with the processor and is adapted to receive, store, and recall data to/from the processor.\n", + "filename": "abstract.txt", + "lastmod": "2020-09-27" }, - "isEmpty": false, - "excerpt": "" - }, - "filename": "sci.md", - "lastmod": "2020-12-04" + "citation.bib": { + "url": "/cv/publications/patents/2017_backfilling/citation.bib", + "path": [ + "publications", + "patents", + "2017_backfilling" + ], + "name": "citation", + "extension": "bib", + "contents": { + "title": "Method for Backfilling Graph Structure and Articles Comprising the Same", + "author": "Bigelow, Alex and Monroe, Megan", + "year": "2017", + "number": "US Patent 9,569,558", + "authorList": [ + "Alex Bigelow", + "Megan Monroe" + ], + "authorLastNames": [ + "Bigelow", + "Monroe" + ], + "joinedAuthorList": "Alex Bigelow and Megan Monroe", + "shortAuthorList": "Bigelow and Monroe", + "howpublished": "US Patent 9,569,558" + }, + "filename": "citation.bib", + "lastmod": "2020-09-27" + } + } }, - "ua.md": { - "url": "/cv/experience/ua.md", - "path": [ - "experience" - ], - "name": "ua", - "extension": "md", - "contents": { - "content": "

As a postdoc, I researched, published, and submitted a grant (that wasn't funded) to study the impacts that different data abstractions can have on visualization design and analysis. I also helped advise two PhD students conducting design studies and building visualization systems for High Performance Computing researchers.

", - "data": { - "title": "Postdoctoral Researcher", - "start": 2019, - "stop": 2021, - "meta": [ - "Department of Computer Science", - "University of Arizona, Tucson, AZ" + "abstracts": { + "2020_pearc": { + "abstract.txt": { + "url": "/cv/publications/abstracts/2020_pearc/abstract.txt", + "path": [ + "publications", + "abstracts", + "2020_pearc" ], - "reference": "Advisor: Dr. Katherine E Isaacs", - "referenceList": [ - "Katherine E Isaacs" - ] + "name": "abstract", + "extension": "txt", + "contents": "We describe an interactive computing environment called JetLag. JetLag implements the following features of Phylanx project: (1) Phylanx, a Python-based asynchronous array computing toolkit; (2) the APEX performance measurement library; (3) a performance visualization framework called Traveler; (4) the Tapis/Agave Science as a Service middleware; and (6) a container infrastructure that includes Docker-based Jupyter notebook for the client and a singularity image for the server. The running system starts with a user performing array computations on their workstation or laptop. If, at some point, the calculation the user is performing becomes sufficiently intensive or numerous, it can be packaged and sent to another machine where it will run (through the batch queue system if there is one), produce a result, and have that result sent back to the user’s local interface. Whether the calculation is local or remote, the user will be able to use APEX and Traveler to diagnose and fix performance related problems. The JetLag system is suitable for a variety of array computational tasks, including machine learning and exploratory data analysis.\n", + "filename": "abstract.txt", + "lastmod": "2020-10-05" }, - "isEmpty": false, - "excerpt": "" - }, - "filename": "ua.md", - "lastmod": "2021-03-13" - }, - "ibm.md": { - "url": "/cv/experience/ibm.md", - "path": [ - "experience" - ], - "name": "ibm", - "extension": "md", - "contents": { - "content": "

During this three-month internship, we developed Jacob's Ladder, a system that supports traversing a large graph database in aggregate using graph pivots.

\n

Apache TinkerPop3 was released midway through this project, just as we had switched from a Neo4j graph database to a Titan database. I learned a lot about graph databases and graph query languages, and learned hard but valuable lessons about good documentation, developing for a moving target, and the dangers of vendor lock-in.

", - "data": { - "title": "Research Intern", - "season": "Summer", - "year": 2015, - "meta": [ - "IBM Research", - "Cambridge, MA" + "citation.bib": { + "url": "/cv/publications/abstracts/2020_pearc/citation.bib", + "path": [ + "publications", + "abstracts", + "2020_pearc" ], - "reference": "Mentor: Dr. Megan Monroe", - "links": { - "PacificVis Paper": "/cv#jacobs_ladder", - "Project": "/projects#jacobs_ladder" + "name": "citation", + "extension": "bib", + "contents": { + "author": "Brandt, Steven R. and Bigelow, Alex and Sakin, Sayef Azad and Williams, Katy and Isaacs, Katherine E. and Huck, Kevin and Tohid, Rod and Wagle, Bibek and Shirzad, Shahrzad and Kaiser, Hartmut", + "title": "JetLag: An Interactive, Asynchronous Array Computing Environment", + "year": "2020", + "isbn": "9781450366892", + "publisher": "Association for Computing Machinery", + "address": "New York, NY, USA", + "url": "https://doi.org/10.1145/3311790.3396657", + "doi": "10.1145/3311790.3396657", + "abstract": "We describe an interactive computing environment called JetLag. JetLag implements the following features of Phylanx project: (1) Phylanx, a Python-based asynchronous array computing toolkit; (2) the APEX performance measurement library; (3) a performance visualization framework called Traveler; (4) the Tapis/Agave Science as a Service middleware; and (6) a container infrastructure that includes Docker-based Jupyter notebook for the client and a singularity image for the server. The running system starts with a user performing array computations on their workstation or laptop. If, at some point, the calculation the user is performing becomes sufficiently intensive or numerous, it can be packaged and sent to another machine where it will run (through the batch queue system if there is one), produce a result, and have that result sent back to the user’s local interface. Whether the calculation is local or remote, the user will be able to use APEX and Traveler to diagnose and fix performance related problems. The JetLag system is suitable for a variety of array computational tasks, including machine learning and exploratory data analysis. ", + "booktitle": "Practice and Experience in Advanced Research Computing", + "pages": "8–12", + "numpages": "5", + "keywords": "performance visualization, interactive computing, research environment, asynchronous, cloud computing, performance tuning, array", + "location": "Portland, OR, USA", + "series": "PEARC '20", + "authorList": [ + "Steven R. Brandt", + "Alex Bigelow", + "Sayef Azad Sakin", + "Katy Williams", + "Katherine E. Isaacs", + "Kevin Huck", + "Rod Tohid", + "Bibek Wagle", + "Shahrzad Shirzad", + "Hartmut Kaiser" + ], + "authorLastNames": [ + "Brandt", + "Bigelow", + "Sakin", + "Williams", + "Isaacs", + "Huck", + "Tohid", + "Wagle", + "Shirzad", + "Kaiser" + ], + "joinedAuthorList": "Steven R. Brandt, Alex Bigelow, Sayef Azad Sakin, Katy Williams, Katherine E. Isaacs, Kevin Huck, Rod Tohid, Bibek Wagle, Shahrzad Shirzad, and Hartmut Kaiser", + "shortAuthorList": "Brandt, Bigelow, Sakin, Williams, Isaacs, Huck, Tohid, Wagle, Shirzad, and Kaiser" }, - "referenceList": [ - "Megan Monroe" - ] + "filename": "citation.bib", + "lastmod": "2020-10-05" }, - "isEmpty": false, - "excerpt": "" + "publication.pdf": { + "url": "/cv/publications/abstracts/2020_pearc/publication.pdf", + "path": [ + "publications", + "abstracts", + "2020_pearc" + ], + "name": "publication", + "extension": "pdf", + "filename": "publication.pdf", + "lastmod": "2020-10-05" + } }, - "filename": "ibm.md", - "lastmod": "2020-12-04" - }, - "stardog.md": { - "url": "/cv/experience/stardog.md", - "path": [ - "experience" - ], - "name": "stardog", - "extension": "md", - "contents": { - "content": "

Since starting at Stardog, I've helped mock up, implement, and deploy a visual network modeling tool, as well as contribute to the development of an existing IDE and network visualization tool.

", - "data": { - "title": "Software Engineer", - "start": 2021, - "stop": "Present", - "meta": [ - "Stardog Union", - "Arlington, VA" + "2013_compariseq": { + "poster.pdf": { + "url": "/cv/publications/abstracts/2013_compariseq/poster.pdf", + "path": [ + "publications", + "abstracts", + "2013_compariseq" + ], + "name": "poster", + "extension": "pdf", + "filename": "poster.pdf", + "lastmod": "2020-09-27" + }, + "citation.bib": { + "url": "/cv/publications/abstracts/2013_compariseq/citation.bib", + "path": [ + "publications", + "abstracts", + "2013_compariseq" + ], + "name": "citation", + "extension": "bib", + "contents": { + "title": "compariSeq: Rethinking Sequence Logos", + "author": "McKenna, Sean and Quinan, Philip S. and Bigelow, Alex", + "year": "2013", + "booktitle": "Proceedings of the 5th Symposium on Biological Data Visualization (BioVis'13)", + "authorList": [ + "Sean McKenna", + "Philip S. Quinan", + "Alex Bigelow" + ], + "authorLastNames": [ + "McKenna", + "Quinan", + "Bigelow" + ], + "joinedAuthorList": "Sean McKenna, Philip S. Quinan, and Alex Bigelow", + "shortAuthorList": "McKenna, Quinan, and Bigelow" + }, + "filename": "citation.bib", + "lastmod": "2020-09-27" + }, + "publication.pdf": { + "url": "/cv/publications/abstracts/2013_compariseq/publication.pdf", + "path": [ + "publications", + "abstracts", + "2013_compariseq" ], - "reference": "Mentors: Annee Barrett, Dr. Jason Rogers, Laura Firey Monroe, Dr. Michael Grove, Paul Ambro", - "referenceList": [ - "Barrett", - "Jason Rogers", - "Laura Firey Monroe", - "Michael Grove", - "Paul Ambro" - ] + "name": "publication", + "extension": "pdf", + "filename": "publication.pdf", + "lastmod": "2020-09-27" }, - "isEmpty": false, - "excerpt": "" + "compariSeq.png": { + "url": "/cv/publications/abstracts/2013_compariseq/compariSeq.png", + "path": [ + "publications", + "abstracts", + "2013_compariseq" + ], + "name": "compariSeq", + "extension": "png", + "filename": "compariSeq.png", + "lastmod": "2020-09-27" + } }, - "filename": "stardog.md", - "lastmod": "2021-09-30" - }, - "kitware.md": { - "url": "/cv/experience/kitware.md", - "path": [ - "experience" - ], - "name": "kitware", - "extension": "md", - "contents": { - "content": "

During this seven-month internship, I was privileged to work on Resonant Lab, a system that enables connecting arbitrary datasets to arbitrary visualizations. This work culminated in a Best Paper Award at the Visualization In Practice Workshop (VIP '16).

\n

I gained a lot of experience with real-world software development, and building better-quality software than I normally have time for in academia was incredibly satisfying. Working in an industry research lab like this was great because it gave me the flexibility to think deeply about problems and approach them in non-conventional ways, but at the same time, it provided the support and priority structure to develop high-quality software. Working for Kitware was also a valuable experience because of its focus on open-source development.

", - "data": { - "title": "Research Intern", - "season": "Spring, Summer", - "year": 2016, - "meta": [ - "Kitware, Inc.", - "Clifton Park, NY" + "2016_vip_resonant_lab": { + "abstract.txt": { + "url": "/cv/publications/abstracts/2016_vip_resonant_lab/abstract.txt", + "path": [ + "publications", + "abstracts", + "2016_vip_resonant_lab" ], - "reference": "Mentors: Dr. Jeff Baumes, Dr. Roni Choudhury", - "links": { - "VIP Best Paper": "/cv#2016_vip_resonant_lab", - "Resonant Lab": "/projects#resonant_lab" - }, - "referenceList": [ - "Jeff Baumes", - "Roni Choudhury" - ] + "name": "abstract", + "extension": "txt", + "contents": "Visualization practitioners are constantly developing new, innovative ways to visualize data, but much of the software that practitioners produce does not make it into production in professional systems. To solve this problem, we have developed and informally tested two open source systems. The first, Candela, is a framework and API for creating visualization components for the web that can wrap up new or existing visualizations as needed. Because Candela’s API generalizes the inputs to a visualization, we have also developed a system called Resonant Laboratory that makes it possible for novice users to connect arbitrary datasets to Candela visualizations. Together, these systems enable novice users to explore and share their data with the growing library of state-of-the-art visualization techniques.\n", + "filename": "abstract.txt", + "lastmod": "2020-09-27" }, - "isEmpty": false, - "excerpt": "" - }, - "filename": "kitware.md", - "lastmod": "2020-12-04" - }, - "ta_1.md": { - "url": "/cv/experience/ta_1.md", - "path": [ - "experience" - ], - "name": "ta_1", - "extension": "md", - "contents": { - "content": "", - "data": { - "title": "Teaching Assistant", - "season": "Fall", - "year": 2014, - "meta": [ - "CS 5630 / 6630 Visualization", - "University of Utah, Salt Lake City, UT" + "award.txt": { + "url": "/cv/publications/abstracts/2016_vip_resonant_lab/award.txt", + "path": [ + "publications", + "abstracts", + "2016_vip_resonant_lab" ], - "reference": "with Dr. Miriah Meyer, using Processing", - "links": { - "Course page": "https://www.cs.utah.edu/~miriah/teaching/cs6630/" - }, - "referenceList": [ - "Miriah Meyer" - ] + "name": "award", + "extension": "txt", + "contents": "Best Paper Award\n", + "filename": "award.txt", + "lastmod": "2020-09-27" }, - "isEmpty": false, - "excerpt": "" - }, - "filename": "ta_1.md", - "lastmod": "2020-12-04" - }, - "brusci.md": { - "url": "/cv/experience/brusci.md", - "path": [ - "experience" - ], - "name": "brusci", - "extension": "md", - "contents": { - "content": "

I volunteered on the SCI Institute's student committee. Responsibilities have included:

\n
    \n
  • Deep involvement in planning and carrying out the SCI X exhibition in 2016. This included creating an interactive map for a display table and visitors' devices
    • \n
  • Planning and carrying out Institute parties. This included mocking up an interface for managing an in-house ping pong tournament
    • \n
", - "data": { - "title": "Committee Member", - "start": 2015, - "stop": 2018, - "service": true, - "meta": [ - "Scientific Computing and Imaging Institute", - "Student Activity Committee", - "University of Utah, Salt Lake City, UT" + "slides.url": { + "url": "/cv/publications/abstracts/2016_vip_resonant_lab/slides.url", + "path": [ + "publications", + "abstracts", + "2016_vip_resonant_lab" ], - "hideInPrint": true, - "reference": "Advisor: Dr. Greg Jones", - "links": { - "SCI X Map": "/projects#scix_map", - "Ping Pong Tournament": "/projects#ping_pong_tournament", - "InfoVis Poster": "/cv#2017_fellow_tool_builders" - }, - "referenceList": [ - "Greg Jones" - ] + "name": "slides", + "extension": "url", + "contents": "http://www.cs.utah.edu/~abigelow/Downloads/papers/VisInPractice2016.key\n", + "filename": "slides.url", + "lastmod": "2020-09-27" }, - "isEmpty": false, - "excerpt": "" - }, - "filename": "brusci.md", - "lastmod": "2021-09-30" - }, - "dsf.md": { - "url": "/cv/experience/dsf.md", - "path": [ - "experience" - ], - "name": "dsf", - "extension": "md", - "contents": { - "content": "

The University of Arizona Data Science Fellow program included a period of intense training in which each fellow instructed the others in specific data science disciplines; for example, in my case, I developed and conducted a series of trainings in data visualization.

\n

We also engaged with University projects in the Health Sciences and adjacent organizations; my involvement included working with Arizona Research Bazaar to help with campus computing outreach efforts, as well as HCW HOSTED to provide resources for healthcare workers during the COVID-19 pandemic.

", - "data": { - "title": "Data Science Fellow", - "start": 2020, - "stop": 2020, - "meta": [ - "Health Sciences", - "University of Arizona, Tucson, AZ" + "citation.bib": { + "url": "/cv/publications/abstracts/2016_vip_resonant_lab/citation.bib", + "path": [ + "publications", + "abstracts", + "2016_vip_resonant_lab" ], - "reference": "Mentors: Dr. Alex Thome, Dr. Maliaca Oxnam, Dr. Eric Lyons", - "links": { - "PLOS Comp. Bio. Paper": "/cv#2020_ten_rules", - "HCW HOSTED Project": "/projects#hcw_hosted", - "Arizona Research Bazaar": "/cv#resbaz" + "name": "citation", + "extension": "bib", + "contents": { + "title": "Resonant Laboratory and Candela: Spreading Your Visualization Ideas to the Masses", + "author": "Bigelow, Alex and Choudhury, Roni and Baumes, Jeffrey", + "booktitle": "Proceedings of the Workshop on Visualization in Practice (VIP'16)", + "year": "2016", + "authorList": [ + "Alex Bigelow", + "Roni Choudhury", + "Jeffrey Baumes" + ], + "authorLastNames": [ + "Bigelow", + "Choudhury", + "Baumes" + ], + "joinedAuthorList": "Alex Bigelow, Roni Choudhury, and Jeffrey Baumes", + "shortAuthorList": "Bigelow, Choudhury, and Baumes" }, - "referenceList": [ - "Alex Thome", - "Maliaca Oxnam", - "Eric Lyons" - ] + "filename": "citation.bib", + "lastmod": "2020-09-27" }, - "isEmpty": false, - "excerpt": "" - }, - "filename": "dsf.md", - "lastmod": "2020-12-04" - } - }, - "publications": { - "patents": { - "2017_backfilling": { - "US9569558.pdf": { - "url": "/cv/publications/patents/2017_backfilling/US9569558.pdf", + "publication.pdf": { + "url": "/cv/publications/abstracts/2016_vip_resonant_lab/publication.pdf", "path": [ "publications", - "patents", - "2017_backfilling" + "abstracts", + "2016_vip_resonant_lab" ], - "name": "US9569558", + "name": "publication", "extension": "pdf", - "filename": "US9569558.pdf", + "filename": "publication.pdf", "lastmod": "2020-09-27" }, + "meta.json": { + "url": "/cv/publications/abstracts/2016_vip_resonant_lab/meta.json", + "path": [ + "publications", + "abstracts", + "2016_vip_resonant_lab" + ], + "name": "meta", + "extension": "json", + "contents": { + "award": "Best Paper Award" + }, + "filename": "meta.json", + "lastmod": "2020-09-27" + } + }, + "2020_pyhpc": { "abstract.txt": { - "url": "/cv/publications/patents/2017_backfilling/abstract.txt", + "url": "/cv/publications/abstracts/2020_pyhpc/abstract.txt", "path": [ "publications", - "patents", - "2017_backfilling" + "abstracts", + "2020_pyhpc" ], "name": "abstract", "extension": "txt", - "contents": "Disclosed herein is system for updating a graph-based data structure comprising a processor that hosts an algorithm to incrementally update underlying data and abstractions for a graph-based data structure based on popular user selections; a user interface that is in two-way operative communication with the processor; where the user interface is operative to present graph-based data structures to a user for updating; and a memory database that is in communication with the processor and is adapted to receive, store, and recall data to/from the processor.\n", + "contents": "We describe JetLag, a Python-based environment that provides access to a distributed, interactive, asynchronous many-task (AMT) computing framework called Phylanx. This environment encompasses the entire computing process, from a Jupyter front-end for managing code and results to the collection and visualization of performance data.\n\nWe use a Python decorator to access the abstract syntax tree of Python functions and transpile them into a set of C++ data structures which are then executed by the HPX runtime. The environment includes services for sending functions and their arguments to run as jobs on remote resources.\n\nA set of Docker and Singularity containers are used to simplify the setup of the JetLag environment. The JetLag system is suitable for a variety of array computational tasks, including machine learning and exploratory data analysis.\n", "filename": "abstract.txt", - "lastmod": "2020-09-27" + "lastmod": "2020-10-16" }, "citation.bib": { - "url": "/cv/publications/patents/2017_backfilling/citation.bib", + "url": "/cv/publications/abstracts/2020_pyhpc/citation.bib", "path": [ "publications", - "patents", - "2017_backfilling" + "abstracts", + "2020_pyhpc" ], "name": "citation", "extension": "bib", "contents": { - "title": "Method for Backfilling Graph Structure and Articles Comprising the Same", - "author": "Bigelow, Alex and Monroe, Megan", - "year": "2017", - "number": "US Patent 9,569,558", + "author": "Brandt, Steven R. and Hasheminezhad, Bita and Wu, Nanmiao and Sakin, Sayef Azad and Bigelow, Alex R. and Isaacs, Katherine E. and Huck, Kevin and Kaiser, Hartmut", + "booktitle": "2020 IEEE/ACM 9th Workshop on Python for High-Performance and Scientific Computing (PyHPC)", + "title": "Distributed Asynchronous Array Computing with the JetLag Environment", + "year": "2020", + "volume": "", + "number": "", + "pages": "49-57", + "doi": "10.1109/PyHPC51966.2020.00011", "authorList": [ - "Alex Bigelow", - "Megan Monroe" + "Steven R. Brandt", + "Bita Hasheminezhad", + "Nanmiao Wu", + "Sayef Azad Sakin", + "Alex R. Bigelow", + "Katherine E. Isaacs", + "Kevin Huck", + "Hartmut Kaiser" ], - "joinedAuthorList": "Alex Bigelow and Megan Monroe", - "howpublished": "US Patent 9,569,558" + "authorLastNames": [ + "Brandt", + "Hasheminezhad", + "Wu", + "Sakin", + "Bigelow", + "Isaacs", + "Huck", + "Kaiser" + ], + "joinedAuthorList": "Steven R. Brandt, Bita Hasheminezhad, Nanmiao Wu, Sayef Azad Sakin, Alex R. Bigelow, Katherine E. Isaacs, Kevin Huck, and Hartmut Kaiser", + "shortAuthorList": "Brandt, Hasheminezhad, Wu, Sakin, Bigelow, Isaacs, Huck, and Kaiser" }, "filename": "citation.bib", - "lastmod": "2020-09-27" + "lastmod": "2022-08-27" } - } - }, - "papers": { - "2014_targeted": { - "abstract.txt": { - "url": "/cv/publications/papers/2014_targeted/abstract.txt", + }, + "2012_comprehengsive": { + "award.txt": { + "url": "/cv/publications/abstracts/2012_comprehengsive/award.txt", "path": [ "publications", - "papers", - "2014_targeted" + "abstracts", + "2012_comprehengsive" ], - "name": "abstract", + "name": "award", "extension": "txt", - "contents": "CASP8 at 2q33 is an established common, low risk susceptibility locus for breast cancer but functional variants are yet to be elucidated. Previously we used haplotype mining of 45 tSNPs in 3778 breast cancer cases and controls to identify a risk haplotype maximizing association evidence. A protective haplotype was also suggested. Here, we perform a focused sequencing study to identify the critical sequence variant/s.\n\nTo not exclude potential regulatory variants, we designed a custom Agilent SureSelect capture array to target all non-repetitive sequence in the 1 Mb region surrounding CASP8. The resulting 41 libraries for germline DNA (24 breast cancer cases homozygous for the risk haplotype, 17 cancer-free women carrying the protective haplotype) were sequenced on the Life Technologies SOLID system. A total of 1464 sequence variants were prioritized by their propensity to lie on the risk or protective haplotypes, resulting in the selection of 42 variants to follow-up with expression-QTL analysis (MAFs 0.1-0.4). Our RNA sequencing panel comprised 156 tissue samples from 88 women (68 breast tumor, 88 normal breast). Illumina TruSeq stranded mRNA sequencing was performed on an Illumina HiSeq 2000. Genotyping for the 42 selected variants was performed using Illumina BeadXpress. RNAseq eQTL analysis focused on 4 genes: CFLAR, CASP10, CASP8, ALS2CR12 using counts standardized to fragments per kilobase per million bases (FPKM). Differences in FPKM between carriers and non-carriers of the 42 DNA sequence variants were assessed in both normal and tumor tissues. Replication analyses were carried out on available TCGA data and published blood eQTL microarray data.\n\nIn normal tissue, an intronic variant in ALS2CR12 on the risk haplotype was best associated with CASP8 expression (19% decreased FPKM, p=9x10-5). Eight other variants (all in ALS2CR12 or CASP8) showed similar CASP8 decreases (p<10-3). Increased ALS2CR12 expression was also observed for the same variants, and decreased CASP8 expression was seen in tumor. Despite the difference in technologies, lower coverage and sparser genotyping, the decreased CASP8 and increased ALS2CR12 levels were replicated in both in the TCGA normal tissue (p=3x10-4) and blood eQTL data (p=4x10-14).\n\nIn tumor, our strongest eQTL results were for decreased expression of CFLAR (p=1x10-4) and CASP10 (p=4x10-5), identified for variants on the protective haplotype (including rs1045485). Examination of TCGA breast tumors did not replicate these findings; however read depths were substantially lower for these genes in the TCGA data.\n\nWe find evidence for two separate paths to 2q33 breast cancer risk. Reduction of CASP8 expression, which may lead to reduced apoptosis and an environment conducive to tumor development. Reduction of CFLAR-CASP10 expression in tumor may implicate autophagy leading to a challenging environment for tumors, but requires more replication.", - "filename": "abstract.txt", - "lastmod": "" + "contents": "Poster selected for oral presentation\n", + "filename": "award.txt", + "lastmod": "2020-09-27" }, "citation.bib": { - "url": "/cv/publications/papers/2014_targeted/citation.bib", + "url": "/cv/publications/abstracts/2012_comprehengsive/citation.bib", "path": [ "publications", - "papers", - "2014_targeted" + "abstracts", + "2012_comprehengsive" ], "name": "citation", "extension": "bib", "contents": { - "title": "Targeted DNA and RNA sequencing identifies breast cancer risk variants associated with differential expression of CASP8 and CFLAR/CASP10", - "author": "Camp, Nicola J. and Lin, Wei-Yu and Bigelow, Alex and Parry, Marina A. and Mosbruger, Tim and Burghel, George and Rajamanickam, Venkatesh and Rigas, Sushilaben H. and Cosby, Rachel and Connley, Dan and Wang, Guoying and Tresa, George and Waller, Rosalie G. and Cannon-Albright, Lisa A. and Brandt, Jones and Sargent, Rob and Reed, Malcolm W. R. and Cox, Angela", - "journal": "Cancer Research", - "volume": "74", - "number": "19\\_Supplement", - "pages": "3267--3267", - "year": "2014", - "publisher": "AACR", + "title": "compreheNGSive: A Tool for Exploring Next-Gen Sequencing Variants", + "author": "Bigelow, Alex and Meyer, Miriah and Camp, Nicola J.", + "year": "2012", + "booktitle": "Proceedings of the IEEE Symposium on Biological Data Visualization (BioVis'12)", "authorList": [ - "Nicola J. Camp", - "Wei-Yu Lin", "Alex Bigelow", - "Marina A. Parry", - "Tim Mosbruger", - "George Burghel", - "Venkatesh Rajamanickam", - "Sushilaben H. Rigas", - "Rachel Cosby", - "Dan Connley", - "Guoying Wang", - "George Tresa", - "Rosalie G. Waller", - "Lisa A. Cannon-Albright", - "Jones Brandt", - "Rob Sargent", - "Malcolm W. R. Reed", - "Angela Cox" + "Miriah Meyer", + "Nicola J. Camp" ], - "joinedAuthorList": "Nicola J. Camp, Wei-Yu Lin, Alex Bigelow, Marina A. Parry, Tim Mosbruger, George Burghel, Venkatesh Rajamanickam, Sushilaben H. Rigas, Rachel Cosby, Dan Connley, Guoying Wang, George Tresa, Rosalie G. Waller, Lisa A. Cannon-Albright, Jones Brandt, Rob Sargent, Malcolm W. R. Reed, and Angela Cox" + "authorLastNames": [ + "Bigelow", + "Meyer", + "Camp" + ], + "joinedAuthorList": "Alex Bigelow, Miriah Meyer, and Nicola J. Camp", + "shortAuthorList": "Bigelow, Meyer, and Camp" }, "filename": "citation.bib", - "lastmod": "" - } - }, - "2020_guidelines": { - "talk.url": { - "url": "/cv/publications/papers/2020_guidelines/talk.url", - "path": [ - "publications", - "papers", - "2020_guidelines" - ], - "name": "talk", - "extension": "url", - "contents": "https://youtu.be/DhPiHvtgtTI\n", - "filename": "talk.url", - "lastmod": "2020-10-23" - }, - "osf.url": { - "url": "/cv/publications/papers/2020_guidelines/osf.url", - "path": [ - "publications", - "papers", - "2020_guidelines" - ], - "name": "osf", - "extension": "url", - "contents": "https://osf.io/s2wmp/\n", - "filename": "osf.url", - "lastmod": "2020-10-23" - }, - "results.url": { - "url": "/cv/publications/papers/2020_guidelines/results.url", - "path": [ - "publications", - "papers", - "2020_guidelines" - ], - "name": "results", - "extension": "url", - "contents": "https://alex-r-bigelow.github.io/wrangling-survey/Responses.html\n", - "filename": "results.url", - "lastmod": "2020-10-23" - }, - "abstract.txt": { - "url": "/cv/publications/papers/2020_guidelines/abstract.txt", - "path": [ - "publications", - "papers", - "2020_guidelines" - ], - "name": "abstract", - "extension": "txt", - "contents": "Many data abstraction types, such as networks or set relationships, remain unfamiliar to data workers beyond the\nvisualization research community. We conduct a survey and series of interviews about how people describe their data, either directly or\nindirectly. We refer to the latter as latent data abstractions. We conduct a Grounded Theory analysis that (1) interprets the extent to\nwhich latent data abstractions exist, (2) reveals the far-reaching effects that the interventionist pursuit of such abstractions can have on\ndata workers, (3) describes why and when data workers may resist such explorations, and (4) suggests how to take advantage of\nopportunities and mitigate risks through transparency about visualization research perspectives and agendas. We then use the themes\nand codes discovered in the Grounded Theory analysis to develop guidelines for data abstraction in visualization projects. To continue\nthe discussion, we make our dataset open along with a visual interface for further exploration.\n", - "filename": "abstract.txt", - "lastmod": "2020-10-05" + "lastmod": "2020-09-27" }, "publication.pdf": { - "url": "/cv/publications/papers/2020_guidelines/publication.pdf", + "url": "/cv/publications/abstracts/2012_comprehengsive/publication.pdf", "path": [ "publications", - "papers", - "2020_guidelines" + "abstracts", + "2012_comprehengsive" ], "name": "publication", "extension": "pdf", "filename": "publication.pdf", - "lastmod": "2020-10-05" + "lastmod": "2020-09-27" }, - "citation.bib": { - "url": "/cv/publications/papers/2020_guidelines/citation.bib", + "meta.json": { + "url": "/cv/publications/abstracts/2012_comprehengsive/meta.json", "path": [ "publications", - "papers", - "2020_guidelines" + "abstracts", + "2012_comprehengsive" ], - "name": "citation", - "extension": "bib", + "name": "meta", + "extension": "json", "contents": { - "title": "Guidelines For Pursuing and Revealing Data Abstractions", - "author": "Bigelow, Alex and Williams, Katy and Isaacs, Katherine E.", - "journal": "IEEE Transactions on Visualization and Computer Graphics", - "year": "2020", - "publisher": "IEEE", - "authorList": [ - "Alex Bigelow", - "Katy Williams", - "Katherine E. Isaacs" - ], - "joinedAuthorList": "Alex Bigelow, Katy Williams, and Katherine E. Isaacs" + "award": "Poster Selected for Oral Presentation" }, - "filename": "citation.bib", - "lastmod": "2020-10-05" + "filename": "meta.json", + "lastmod": "2020-09-27" } }, - "2019_infovis_atria": { - "talk.url": { - "url": "/cv/publications/papers/2019_infovis_atria/talk.url", + "2017_fellow_tool_builders": { + "poster.pdf": { + "url": "/cv/publications/abstracts/2017_fellow_tool_builders/poster.pdf", "path": [ "publications", - "papers", - "2019_infovis_atria" + "abstracts", + "2017_fellow_tool_builders" ], - "name": "talk", - "extension": "url", - "contents": "https://vimeo.com/370668837\n", - "filename": "talk.url", - "lastmod": "2020-10-23" + "name": "poster", + "extension": "pdf", + "filename": "poster.pdf", + "lastmod": "2020-09-27" }, "abstract.txt": { - "url": "/cv/publications/papers/2019_infovis_atria/abstract.txt", + "url": "/cv/publications/abstracts/2017_fellow_tool_builders/abstract.txt", "path": [ "publications", - "papers", - "2019_infovis_atria" + "abstracts", + "2017_fellow_tool_builders" ], "name": "abstract", "extension": "txt", - "contents": "Common pitfalls in visualization projects include lack of data availability and the domain users’ needs and focus changing too rapidly for the design process to complete. While it is often prudent to avoid such projects, we argue it can be beneficial to engage them in some cases as the visualization process can help refine data collection, solving a “chicken and egg” problem of having the data and tools to analyze it. We found this to be the case in the domain of task parallel computing where such data and tooling is an open area of research. Despite these hurdles, we conducted a design study. Through a tightly-coupled iterative design process, we built Atria, a multi-view execution graph visualization to support performance analysis. Atria simplifies the initial representation of the execution graph by aggregating nodes as related to their line of code. We deployed Atria on multiple platforms, some requiring design alteration. We describe how we adapted the design study methodology to the “moving target” of both the data and the domain experts’ concerns and how this movement kept both the visualization and programming project healthy. We reflect on our process and discuss what factors allow the project to be successful in the presence of changing data and user needs.\n", + "contents": "While it is true that fellow tool builders can threaten the success of a design study, there are also advantages to working with individuals that have strong software development skills. We present a review of two information visualization projects using thematic analysis, that provides additional insight and guidance for collaborating with people that have strong software development skills. Additionally, we discuss minor implications for the design of node-link diagrams and adjacency matrices, and report observed differences in engagement with respect to touch tables versus traditional keyboard, mouse, and monitor configurations.\n", "filename": "abstract.txt", "lastmod": "2020-09-27" }, - "publication.pdf": { - "url": "/cv/publications/papers/2019_infovis_atria/publication.pdf", - "path": [ - "publications", - "papers", - "2019_infovis_atria" - ], - "name": "publication", - "extension": "pdf", - "filename": "publication.pdf", - "lastmod": "2020-09-27" - }, - "citation.bib": { - "url": "/cv/publications/papers/2019_infovis_atria/citation.bib", + "supplement.md": { + "url": "/cv/publications/abstracts/2017_fellow_tool_builders/supplement.md", "path": [ "publications", - "papers", - "2019_infovis_atria" + "abstracts", + "2017_fellow_tool_builders" ], - "name": "citation", - "extension": "bib", + "name": "supplement", + "extension": "md", "contents": { - "title": "Visualizing a Moving Target: A Design Study on Task Parallel Programs in the Presence of Evolving Data and Concerns", - "author": "Williams, Katy and Bigelow, Alex and Isaacs, Katherine E.", - "journal": "IEEE Transactions on Visualization and Computer Graphics", - "volume": "26", - "number": "1", - "pages": "1118--1128", - "year": "2019", - "publisher": "IEEE", - "doi": "10.1109/TVCG.2019.2934285", - "authorList": [ - "Katy Williams", - "Alex Bigelow", - "Katherine E. Isaacs" - ], - "joinedAuthorList": "Katy Williams, Alex Bigelow, and Katherine E. Isaacs" + "content": "

This file summarizes the raw observations, open codes, and resulting themes.

\n

Collaborators

\n

| ID | Role | Gender | Research Area |\n|--------|---------------------|--------|---------------------------|\n| I1 | Mid Grad Student | F | Biomedical Computation |\n| I2 | Mid Grad Student | F | Biomedical Computation |\n| I3 | Staff Developer | F | Scientific Computing |\n| I4 | Research Faculty | M | Information Visualization |\n| I5 | Senior Grad Student | M | Biomedical Computation |\n| I6 | Senior Grad Student | M | Biomedical Computation |\n| I7 | Senior Grad Student | M | Biomedical Computation |\n| I8 | New Grad Student | F | Scientific Visualization |

\n

Raw observations

\n

The very raw data used for this poster takes the form of git commit messages, git histories, emails, Slack conversations, and group meeting notes.\nRather than include all of that data directly (that would include identifying information, etc), extracts of the raw events surrounding the development of each system are summarized below.

\n

Open House Map Extracts

\n
    \n
  • M1: We used text CSV files on GitHub to hold all the information about what groups would be where, and, later, what individual posters or presentations would be in what area. These csv files had to be refactored a number of times
    • \n
  • M2: Though the student committee worked hard for weeks to get details, I ended up having to come in at night to collect poster location information myself, once the posters were finally set up. I3's assigned area was particularly problematic, because the location was changed last-minute
    • \n
  • M3: Using an Illustrator SVG map made annotating (e.g. adding restrooms to the map) / changing area shapes easy; most changes in the git history were changes to the spaceAssignments.csv file
    • \n
  • M4: I4 provided useful feedback about the width of the selection bars above each poster name (they were initially squares and hard to click directly, even though the whole text block was technically clickable), but also provided (too much?) feedback about things like typography
    • \n
  • M5: An institution-wide meeting (mostly about making sure people created / printed their posters on time) quickly devolved into a debate about the interface… particularly with respect to the map orientation (should North be up? But people exit the elevator, and initially encounter the interactive interface facing South…). However, an important development in this meeting occurred when the task abstraction of the interface changed---some participants indicated that they knew specific visitors that would want to be able to locate individual posters.
    • \n
  • M6: Public display on a touch table likely contributed to high engagement - my personal demo was on an equally-sized monitor immediately off the elevator, but most visitors would walk right past me to the touch display in the room behind me (of course, I didn't actively try to stop people to see my demo, and it makes sense that people would want to first orient themselves in a new environment)
    • \n
\n

Ping Pong Tournament Extracts

\n
    \n
  • P1: Instead of CSV files on GitHub, we used Google forms / sheets as a pseudo-database for the ping pong tournament. We still used GitHub for hosting the site, but this meant that committee members could check / edit the spreadsheets easily
    • \n
  • P2: Setting up a debug / simulation mode was helpful during the live ping pong deployment - I6 in particular responded quickly to requests to beta test changes to the site before they went live. Because of the google spreadsheets setup, it was easy to see and debug what tests he used to try (and, in some cases, succeed) to trigger bugs.
    • \n
  • P3: I5, I6, and I7 had very specific ideas of how the pool play / bracket should work. As such, I planned (and succeeded) to outsource the seeding of the bracket to them via a Google spreadsheet
    • \n
  • P4: Shortly after the first debugging deployment, I8 designed and printed promotional posters using the background image… but chose a very different font style and color scheme. Rather than reprint the posters, we felt it best to refactor the interactive system.
    • \n
  • P5: This interface required typing in information---initially, we planned to deploy the interface on a touch table, as we had with the open house map. The touch table has a built-in keyboard that can be swiped in from the side---but we needed to add an icon to the interface to make this clear. However, due to a more important project needing the touch table, we had to instead deploy the interface on a monitor by the elevator (actually the same monitor where I gave my demo in the open house), with a keyboard and mouse attached
    • \n
  • P6: We initially anticipated more participants---because the limited number that actually signed up was much lower (the vis deadline was partly to blame---we later heard that many more would have signed up, but they were too busy with submissions), we decided to include everyone in the bracket. This necessitated a last-minute rewrite of the code to include BYE / PASS nodes for the highest-seeded players
    • \n
  • P7: It proved difficult to get people to actually play their games, particularly when the scheduled players didn't know each other well. Eventually, we had to add forfeits to the pool play phase (again, necessitating a last-minute redesign of the system). This happened again in the bracket---some students began leaving for the summer. Luckily, the few that had left were able to nominate the player they had most recently defeated to play for them, and the change was a simple adjustment to the spreadsheets (more drastic rewrites of the system were not necessary)
    • \n
  • P8: Our initial plan was for all participants to pick a charity to represent (I1 provided a CSV list of 503(c)(3) charities), and non-players could still participate by \"betting\" on players. However, this garnered little attention / participation. Toward the beginning of the bracket phase, I6 suggested that we implement a March Madness-style approach, where people could submit their own brackets, and award a secondary prize to the charity picked by the most accurate bracket. Unfortunately, this was too difficult to implement in the short amount of time left in the tournament.
    • \n
  • P9: Having the public display also appeared to result in high engagement, though not as much as I observed with the touch table. Passers-by seemed to be hesitant to use the keyboard / mouse… this may have had something to do with the permanent nature of the display (attached to the wall) - normally, the monitor showed a looping video of demonstrations, that people would not normally interfere with.
    • \n
  • P10: Some passers-by reported confusion about the triangular edges, particularly in the node-link diagram (are triangles arrowheads pointing to the winner, or does the larger side indicate the winner)?
    • \n
  • P11: Though most people that interacted with the interface were very technically savvy, the pool play adjacency matrices proved confusing to some people (not all, however… some people even commented on how intuitive they were). In their design, I3 provided very useful feedback---initially, I displayed an arrow for an already-played game, pointing to the winner. However, I3 made it clear that this was confusing; instead, redundantly displaying the name of the winner in the cell made more sense.
    • \n
  • P12: I6 contributed a very minor code fix
    • \n
\n

Open Codes

\n
    \n
  • O1: Last-minute system adjustments were common (M2, P4, P5, P6, P7, P8)
    • \n
  • O2: Clever engineering tricks made most last-minute adjustments easier to handle (M3, P1, P2, P7)
    • \n
  • O3: Actual code contributions from collaborators were rare (P12)
    • \n
  • O4: Spreadsheets encouraged more collaborator help (M1, P1)
    • \n
  • O5: Overall, mixed results getting data from collaborators (M2, P2, P3, P8)
    • \n
  • O6: Confusion about triangular edges (P10)
    • \n
  • O7: Confusion / intuition about rotated adjacency matrices (P11)
    • \n
  • O8: Collaborators' feedback (mostly) insightful (M4, M5, P2, P11)
    • \n
  • O9: Touch table more engaging than monitor + keyboard / mouse (M6, P9)
    • \n
\n

Themes

\n

Collaborator Participation

\n
    \n
  • A1: Collaborator technical involvement in the project varied; personality seemed to dictate whether and how much people contributed, rather than interest in the overall project or interest in the technical aspects (O3, O4, O5). Technical involvement did not seem to have any relationship with relevant technical skills (O3; I6 is not a web developer).
    • \n
  • A2: Collaborators most readily participated when the tools were familiar; google sheets (even with strict rules about structure) were the most freely adjusted. Github CSV files came in second, beta testing the interface itself came in third, and the interface code was barely touched (O3, O4, O5).
    • \n
\n

Collaborator Feedback

\n
    \n
  • A3: Most feedback was helpful; compared to non-developer users in typical design studies, people seemed more willing to provide critique (O8). The kinds of critique that collaborators suggested tended to be more bounded by their technical knowledge of what is easily changed, and what is difficult to implement (01, 02, 08)
    • \n
  • A4: Some feedback was too specific or failed to capture the scope of the project; dealing with this gracefully is tricky. However, it was a pitfall to automatically assume that all feedback was too specific (O8)
    • \n
\n

Implications for Visualization Techniques and Deployment

\n
    \n
  • A5: Adjacency matrices were confusing to a subset of a technical audience (O7)! Artifact of rotated design?
    • \n
  • A6: Triangles as arrows are ambiguous (O6)
    • \n
  • A7: Touch table more engaging than fixed monitor (O9)
    • \n
\n

Key Takeaways

\n
    \n
  • Just because a collaborator has the technical ability and the time to contribute, that doesn't mean that they will (A1, A2)
    • \n
  • The opposite is also true: just because a collaborator doesn't appear to have the technical ability or the time to contribute, that doesn't mean that they won't (A1, A2)
    • \n
  • Concern about working with fellow tool builders is warranted, but they should not necessarily be avoided---their expertise can be an incredible asset (A3, A4)
    • \n
  • Some minor details of node-link diagrams and adjacency matrices can have a profound effect on the ability of users to make sense of what is represented (A5, A6)---where these are employed, a legend is probably necessary
    • \n
  • Touch table vs traditional display: the former seems to naturally produce more engagement / willingness to mess with the system (A7)
    • \n
", + "data": {}, + "isEmpty": false, + "excerpt": "" }, - "filename": "citation.bib", - "lastmod": "2020-10-05" - } - }, - "2022_traveler": { - "abstract.txt": { - "url": "/cv/publications/papers/2022_traveler/abstract.txt", + "filename": "supplement.md", + "lastmod": "2020-09-27" + }, + "fastForward.mp4": { + "url": "/cv/publications/abstracts/2017_fellow_tool_builders/fastForward.mp4", "path": [ "publications", - "papers", - "2022_traveler" + "abstracts", + "2017_fellow_tool_builders" ], - "name": "abstract", - "extension": "txt", - "contents": "Understanding the behavior of software in execution is a key step in identifying and fixing performance issues. This is especially important in high performance computing contexts where even minor performance tweaks can translate into large savings in terms of computational resource use. To aid performance analysis, developers may collect an execution trace - a chronological log of program activity during execution. As traces represent the full history, developers can discover a wide array of possibly previously unknown performance issues, making them an important artifact for exploratory performance analysis. However, interactive trace visualization is difficult due to issues of data size and complexity of meaning. Traces represent nanosecond-level events across many parallel processes, meaning the collected data is often large and difficult to explore. The rise of asynchronous task parallel programming paradigms complicates the relation between events and their probable cause. To address these challenges, we conduct a continuing design study in collaboration with high performance computing researchers. We develop diverse and hierarchical ways to navigate and represent execution trace data in support of their trace analysis tasks. Through an iterative design process, we developed Traveler, an integrated visualization platform for task parallel traces. Traveler provides multiple linked interfaces to help navigate trace data from multiple contexts. We evaluate the utility of Traveler through feedback from users and a case study, finding that integrating multiple modes of navigation in our design supported performance analysis tasks and led to the discovery of previously unknown behavior in a distributed array library.", - "filename": "abstract.txt", - "lastmod": "" + "name": "fastForward", + "extension": "mp4", + "filename": "fastForward.mp4", + "lastmod": "2020-09-27" }, "citation.bib": { - "url": "/cv/publications/papers/2022_traveler/citation.bib", + "url": "/cv/publications/abstracts/2017_fellow_tool_builders/citation.bib", "path": [ "publications", - "papers", - "2022_traveler" + "abstracts", + "2017_fellow_tool_builders" ], "name": "citation", "extension": "bib", "contents": { - "title": "Traveler: Navigating Task Parallel Traces for Performance Analysis", - "author": "Sakin, Sayef Azad and Bigelow, Alex and Tohid, R and Scully-Allison, Connor and Scheidegger, Carlos and Brandt, Steven R. and Taylor, Christopher and Huck, Kevin A. and Kaiser, Hartmut and Isaacs, Katherine E.", - "journal": "arXiv preprint arXiv:2208.00109", - "year": "2022", + "title": "Reflections on Working With Fellow Tool Builders", + "author": "Bigelow, Alex", + "year": "2017", + "booktitle": "Proceedings of the IEEE Information Visualization Conference-Posters (InfoVis'17)", "authorList": [ - "Sayef Azad Sakin", - "Alex Bigelow", - "R Tohid", - "Connor Scully-Allison", - "Carlos Scheidegger", - "Steven R. Brandt", - "Christopher Taylor", - "Kevin A. Huck", - "Hartmut Kaiser", - "Katherine E. Isaacs" + "Alex Bigelow" + ], + "authorLastNames": [ + "Bigelow" ], - "joinedAuthorList": "Sayef Azad Sakin, Alex Bigelow, R Tohid, Connor Scully-Allison, Carlos Scheidegger, Steven R. Brandt, Christopher Taylor, Kevin A. Huck, Hartmut Kaiser, and Katherine E. Isaacs" + "joinedAuthorList": "Alex Bigelow", + "shortAuthorList": "Bigelow" }, "filename": "citation.bib", - "lastmod": "" + "lastmod": "2020-09-27" + }, + "publication.pdf": { + "url": "/cv/publications/abstracts/2017_fellow_tool_builders/publication.pdf", + "path": [ + "publications", + "abstracts", + "2017_fellow_tool_builders" + ], + "name": "publication", + "extension": "pdf", + "filename": "publication.pdf", + "lastmod": "2020-09-27" + }, + "video.mp4": { + "url": "/cv/publications/abstracts/2017_fellow_tool_builders/video.mp4", + "path": [ + "publications", + "abstracts", + "2017_fellow_tool_builders" + ], + "name": "video", + "extension": "mp4", + "filename": "video.mp4", + "lastmod": "2020-09-27" } }, - "2014_avi_reflections": { - "slides.url": { - "url": "/cv/publications/papers/2014_avi_reflections/slides.url", + "2018_murejs": { + "poster.pdf": { + "url": "/cv/publications/abstracts/2018_murejs/poster.pdf", "path": [ "publications", - "papers", - "2014_avi_reflections" + "abstracts", + "2018_murejs" ], - "name": "slides", - "extension": "url", - "contents": "http://sci.utah.edu/~vdl/papers/2014_avi_reflections_slides.pdf\n", - "filename": "slides.url", + "name": "poster", + "extension": "pdf", + "filename": "poster.pdf", "lastmod": "2020-09-27" }, "abstract.txt": { - "url": "/cv/publications/papers/2014_avi_reflections/abstract.txt", + "url": "/cv/publications/abstracts/2018_murejs/abstract.txt", "path": [ "publications", - "papers", - "2014_avi_reflections" + "abstracts", + "2018_murejs" ], "name": "abstract", "extension": "txt", - "contents": "In recent years many popular data visualizations have emerged that are created largely by designers whose main area of expertise is not computer science. Designers generate these visualizations using a handful of design tools and environments. To better inform the development of tools intended for designers working with data, we set out to understand designers’ challenges and perspectives. We interviewed professional designers, conducted observations of designers working with data in the lab, and observed designers working with data in team settings in the wild. A set of patterns emerged from these observations from which we extract a number of themes that provide a new perspective on design considerations for visualization tool creators, as well as on known engineering problems.\n", + "contents": "When interpreting data as a graph for visualization, an analyst first assigns semantic meaning to graph concepts. For example, they may choose to represent actors and movies as nodes, and roles as edges. Alternatively, they may wish to represent movies as edges, connecting actor nodes when they collaborate. Data abstraction choices such as these are critical, because different data abstractions can limit—or inspire—different analysis questions, approaches, perspectives, and visualizations.\n\nHowever, current network modeling frameworks, systems, and databases narrowly define graph abstraction constructs—such as nodes, edges, node / edge classes, supernodes, hyperedges, etc.—in terms of how the data is stored in memory or on disk, rather than semantic, human-driven abstractions. Consequently, the ability of an analyst to iterate on a data abstraction becomes fundamentally limited by the implementation details of data wrangling software.\n\nWe present work-in-progress toward a broader framework for modeling network data that is less dependent on its underlying structure and storage. Our goal is to use semantic data abstraction constructs to inform how algorithms wrangle data, instead of allowing algorithmic concerns to define and constrain the semantics.\n\nWe also present mure.js, a software library that represents an initial implementation of this framework, allowing users to map semantic graph constructs to arbitrary data structures as metadata, that can, in turn, be used to select, navigate, and reshape the under- lying data. Additionally, we discuss an early software prototype of a visual graph wrangling system based on this library.\n", "filename": "abstract.txt", "lastmod": "2020-09-27" }, - "publication.pdf": { - "url": "/cv/publications/papers/2014_avi_reflections/publication.pdf", + "fastForward.mp4": { + "url": "/cv/publications/abstracts/2018_murejs/fastForward.mp4", "path": [ "publications", - "papers", - "2014_avi_reflections" + "abstracts", + "2018_murejs" ], - "name": "publication", - "extension": "pdf", - "filename": "publication.pdf", + "name": "fastForward", + "extension": "mp4", + "filename": "fastForward.mp4", "lastmod": "2020-09-27" }, "citation.bib": { - "url": "/cv/publications/papers/2014_avi_reflections/citation.bib", + "url": "/cv/publications/abstracts/2018_murejs/citation.bib", "path": [ "publications", - "papers", - "2014_avi_reflections" + "abstracts", + "2018_murejs" ], "name": "citation", "extension": "bib", "contents": { - "title": "Reflections on How Designers Design with Data", - "author": "Bigelow, Alex and Drucker, Steven and Fisher, Danyel and Meyer, Miriah", - "booktitle": "Proceedings of the 2014 International Working Conference on Advanced Visual Interfaces", - "pages": "17--24", - "year": "2014", - "organization": "ACM", - "doi": "10.1145/2598153.2598175", + "title": "Mure. js: Toward Flexible Authoring and Reshaping of Networks", + "author": "Bigelow, Alex and Nobre, Carolina and Lex, Alexander and Meyer, Miriah", + "year": "2018", + "booktitle": "Proceedings of the IEEE Information Visualization Conference-Posters (InfoVis'18)", "authorList": [ "Alex Bigelow", - "Steven Drucker", - "Danyel Fisher", + "Carolina Nobre", + "Alexander Lex", "Miriah Meyer" ], - "joinedAuthorList": "Alex Bigelow, Steven Drucker, Danyel Fisher, and Miriah Meyer" + "authorLastNames": [ + "Bigelow", + "Nobre", + "Lex", + "Meyer" + ], + "joinedAuthorList": "Alex Bigelow, Carolina Nobre, Alexander Lex, and Miriah Meyer", + "shortAuthorList": "Bigelow, Nobre, Lex, and Meyer" }, "filename": "citation.bib", - "lastmod": "2020-10-05" - }, - "award.txt": { - "url": "/cv/publications/papers/2014_avi_reflections/award.txt", - "path": [ - "publications", - "papers", - "2014_avi_reflections" - ], - "name": "award", - "extension": "txt", - "contents": "Best Paper Award\n", - "filename": "award.txt", "lastmod": "2020-09-27" }, - "supplement.zip": { - "url": "/cv/publications/papers/2014_avi_reflections/supplement.zip", + "poster.svg": { + "url": "/cv/publications/abstracts/2018_murejs/poster.svg", "path": [ "publications", - "papers", - "2014_avi_reflections" + "abstracts", + "2018_murejs" ], - "name": "supplement", - "extension": "zip", - "filename": "supplement.zip", + "name": "poster", + "extension": "svg", + "filename": "poster.svg", "lastmod": "2020-09-27" }, - "meta.json": { - "url": "/cv/publications/papers/2014_avi_reflections/meta.json", + "publication.pdf": { + "url": "/cv/publications/abstracts/2018_murejs/publication.pdf", "path": [ "publications", - "papers", - "2014_avi_reflections" + "abstracts", + "2018_murejs" ], - "name": "meta", - "extension": "json", - "contents": { - "award": "Best Paper Award" - }, - "filename": "meta.json", + "name": "publication", + "extension": "pdf", + "filename": "publication.pdf", "lastmod": "2020-09-27" } - }, - "2016_infovis_hanpuku": { - "slides.url": { - "url": "/cv/publications/papers/2016_infovis_hanpuku/slides.url", + } + }, + "posters": { + "2015_bob_ross": { + "poster.pdf": { + "url": "/cv/publications/posters/2015_bob_ross/poster.pdf", "path": [ "publications", - "papers", - "2016_infovis_hanpuku" + "posters", + "2015_bob_ross" ], - "name": "slides", - "extension": "url", - "contents": "http://www.cs.utah.edu/~abigelow/Downloads/papers/VisInPractice2016.key\n", - "filename": "slides.url", + "name": "poster", + "extension": "pdf", + "filename": "poster.pdf", "lastmod": "2020-09-27" }, - "talk.url": { - "url": "/cv/publications/papers/2016_infovis_hanpuku/talk.url", + "citation.bib": { + "url": "/cv/publications/posters/2015_bob_ross/citation.bib", "path": [ "publications", - "papers", - "2016_infovis_hanpuku" + "posters", + "2015_bob_ross" ], - "name": "talk", - "extension": "url", - "contents": "https://vimeo.com/201779979\n", - "filename": "talk.url", - "lastmod": "2020-10-23" + "name": "citation", + "extension": "bib", + "contents": { + "title": "Happy Accidents: Analyzing the Paintings of Bob Ross", + "author": "Warner, Ally and Dunstan, Jonathan and Bigelow, Alex", + "howpublished": "University of Utah Data Mining Class Project", + "year": "2015", + "authorList": [ + "Ally Warner", + "Jonathan Dunstan", + "Alex Bigelow" + ], + "authorLastNames": [ + "Warner", + "Dunstan", + "Bigelow" + ], + "joinedAuthorList": "Ally Warner, Jonathan Dunstan, and Alex Bigelow", + "shortAuthorList": "Warner, Dunstan, and Bigelow" + }, + "filename": "citation.bib", + "lastmod": "2020-09-27" }, - "demo.url": { - "url": "/cv/publications/papers/2016_infovis_hanpuku/demo.url", + "publication.pdf": { + "url": "/cv/publications/posters/2015_bob_ross/publication.pdf", "path": [ "publications", - "papers", - "2016_infovis_hanpuku" + "posters", + "2015_bob_ross" ], - "name": "demo", - "extension": "url", - "contents": "https://youtu.be/eNoDZcs7vVs\n", - "filename": "demo.url", - "lastmod": "2020-12-04" - }, - "abstract.txt": { - "url": "/cv/publications/papers/2016_infovis_hanpuku/abstract.txt", + "name": "publication", + "extension": "pdf", + "filename": "publication.pdf", + "lastmod": "2020-09-27" + } + }, + "2014_reflections": { + "poster.pdf": { + "url": "/cv/publications/posters/2014_reflections/poster.pdf", "path": [ "publications", - "papers", - "2016_infovis_hanpuku" + "posters", + "2014_reflections" ], - "name": "abstract", - "extension": "txt", - "contents": "A common workflow for visualization designers begins with a generative tool, like D3 or Processing, to create the initial visualization; and proceeds to a drawing tool, like Adobe Illustrator or Inkscape, for editing and cleaning. Unfortunately, this is typically a one-way process: once a visualization is exported from the generative tool into a drawing tool, it is difficult to make further, data-driven changes. In this paper, we propose a bridge model to allow designers to bring their work back from the drawing tool to re-edit in the generative tool. Our key insight is to recast this iteration challenge as a merge problem - similar to when two people are editing a document and changes between them need to reconciled. We also present a specific instantiation of this model, a tool called Hanpuku, which bridges between D3 scripts and Illustrator. We show several examples of visualizations that are iteratively created using Hanpuku in order to illustrate the flexibility of the approach. We further describe several hypothetical tools that bridge between other visualization tools to emphasize the generality of the model.\n", - "filename": "abstract.txt", + "name": "poster", + "extension": "pdf", + "filename": "poster.pdf", "lastmod": "2020-09-27" }, - "publication.pdf": { - "url": "/cv/publications/papers/2016_infovis_hanpuku/publication.pdf", + "award.txt": { + "url": "/cv/publications/posters/2014_reflections/award.txt", "path": [ "publications", - "papers", - "2016_infovis_hanpuku" + "posters", + "2014_reflections" ], - "name": "publication", - "extension": "pdf", - "filename": "publication.pdf", + "name": "award", + "extension": "txt", + "contents": "Best Poster Award\n", + "filename": "award.txt", "lastmod": "2020-09-27" }, "citation.bib": { - "url": "/cv/publications/papers/2016_infovis_hanpuku/citation.bib", + "url": "/cv/publications/posters/2014_reflections/citation.bib", "path": [ "publications", - "papers", - "2016_infovis_hanpuku" + "posters", + "2014_reflections" ], "name": "citation", "extension": "bib", "contents": { - "title": "Iterating Between Tools to Create and Edit Visualizations", + "title": "Reflections on How Designers Design With Data", "author": "Bigelow, Alex and Drucker, Steven and Fisher, Danyel and Meyer, Miriah", - "journal": "IEEE Transactions on Visualization and Computer Graphics", - "volume": "23", - "number": "1", - "pages": "481--490", - "year": "2016", - "publisher": "IEEE", - "doi": "10.1109/TVCG.2016.2598609", + "howpublished": "University of Utah School of Computing Poster Competition", + "year": "2014", "authorList": [ "Alex Bigelow", "Steven Drucker", "Danyel Fisher", "Miriah Meyer" ], - "joinedAuthorList": "Alex Bigelow, Steven Drucker, Danyel Fisher, and Miriah Meyer" + "authorLastNames": [ + "Bigelow", + "Drucker", + "Fisher", + "Meyer" + ], + "joinedAuthorList": "Alex Bigelow, Steven Drucker, Danyel Fisher, and Miriah Meyer", + "shortAuthorList": "Bigelow, Drucker, Fisher, and Meyer" }, "filename": "citation.bib", - "lastmod": "2020-10-05" - }, - "fastForward.mp4": { - "url": "/cv/publications/papers/2016_infovis_hanpuku/fastForward.mp4", - "path": [ - "publications", - "papers", - "2016_infovis_hanpuku" - ], - "name": "fastForward", - "extension": "mp4", - "filename": "fastForward.mp4", - "lastmod": "2020-09-27" + "lastmod": "2022-08-27" }, - "supplement.zip": { - "url": "/cv/publications/papers/2016_infovis_hanpuku/supplement.zip", + "meta.json": { + "url": "/cv/publications/posters/2014_reflections/meta.json", "path": [ "publications", - "papers", - "2016_infovis_hanpuku" + "posters", + "2014_reflections" ], - "name": "supplement", - "extension": "zip", - "filename": "supplement.zip", + "name": "meta", + "extension": "json", + "contents": { + "award": "Best Poster Award" + }, + "filename": "meta.json", "lastmod": "2020-09-27" } }, - "2016_haplotype": { - "abstract.txt": { - "url": "/cv/publications/papers/2016_haplotype/abstract.txt", + "2015_hanpuku": { + "poster.pdf": { + "url": "/cv/publications/posters/2015_hanpuku/poster.pdf", "path": [ "publications", - "papers", - "2016_haplotype" + "posters", + "2015_hanpuku" ], - "name": "abstract", - "extension": "txt", - "contents": "The findings from genome-wide association studies hold enormous potential for novel insight into disease mechanisms. A major challenge in the field is to map these low-risk association signals to their underlying functional sequence variants(FSV). Simple sequence study designs are insufficient, as the vast numbers of statistically comparable variants and a limited knowledge of noncoding regulatory elements complicate prioritization. Furthermore, large sample sizes are typically required for adequate power to identify the initial association signals. One important question is whether similar sample sizes need to be sequenced to identify the FSVs. Here, we present a proof-of-principle example of an extreme discordant design to map FSVs within the 2q33 low-risk breast cancer locus. Our approach employed DNA sequencing of a small number of discordant haplotypes to efficiently identify candidate FSVs. Our results were consistent with those from a 2,000-fold larger, traditional imputation-based fine-mapping study. To prioritize further, we used expression-quantitative trait locus analysis of RNA sequencing from breast tissues, gene regulation annotations from the ENCODE consortium, and functional assays for differential enhancer activities. Notably, we implicate three regulatory variants at 2q33 that target CASP8 (rs3769823,rs3769821 in CASP8, and rs10197246 in ALS2CR12) as functionally relevant. We conclude that nested discordant haplotype sequencing is a promising approach to aid mapping of low-risk association loci. The ability to include more efficient sequencing designs into mapping efforts presents an opportunity for the field to capitalize on the potential of association loci and accelerate translation of association signals to their underlying FSVs.\n", - "filename": "abstract.txt", + "name": "poster", + "extension": "pdf", + "filename": "poster.pdf", "lastmod": "2020-09-27" }, "citation.bib": { - "url": "/cv/publications/papers/2016_haplotype/citation.bib", + "url": "/cv/publications/posters/2015_hanpuku/citation.bib", "path": [ "publications", - "papers", - "2016_haplotype" + "posters", + "2015_hanpuku" ], "name": "citation", "extension": "bib", "contents": { - "title": "Discordant Haplotype Sequencing Identifies Functional Variants at the 2q33 Breast Cancer Risk Locus", - "author": "Camp, Nicola J. and Lin, Wei-Yu and Bigelow, Alex and Burghel, George J. and Mosbruger, Timothy L. and Parry, Marina A. and Waller, Rosalie G. and Rigas, Sushilaben H. and Tai, Pei-Yi and Berrett, Kristofer and Rajamanickam, Venkatesh and Cosby, Rachel and Brock, Ian W. and Jones, Brandt and Conneley, Dan and Sargent, Robert and Wang, Guoying and Factor, Rachel E. and Bernard, Philip S. and Cannon-Albright, Lisa A. and Knight, Stacey and Abo, Ryan and Werner, Theresa and Reed, Malcolm W. R. and Gertz, Jason and Cox, Angela", - "journal": "Cancer research", - "volume": "76", - "number": "7", - "pages": "1916--1925", - "year": "2016", - "publisher": "AACR", + "title": "A Bridge Supporting Iteration Between Data Exploration and Data Storytelling", + "author": "Bigelow, Alex and Drucker, Steven and Fisher, Danyel and Meyer, Miriah", + "howpublished": "University of Utah School of Computing Poster Competition", + "year": "2015", "authorList": [ - "Nicola J. Camp", - "Wei-Yu Lin", "Alex Bigelow", - "George J. Burghel", - "Timothy L. Mosbruger", - "Marina A. Parry", - "Rosalie G. Waller", - "Sushilaben H. Rigas", - "Pei-Yi Tai", - "Kristofer Berrett", - "Venkatesh Rajamanickam", - "Rachel Cosby", - "Ian W. Brock", - "Brandt Jones", - "Dan Conneley", - "Robert Sargent", - "Guoying Wang", - "Rachel E. Factor", - "Philip S. Bernard", - "Lisa A. Cannon-Albright", - "Stacey Knight", - "Ryan Abo", - "Theresa Werner", - "Malcolm W. R. Reed", - "Jason Gertz", - "Angela Cox" + "Steven Drucker", + "Danyel Fisher", + "Miriah Meyer" + ], + "authorLastNames": [ + "Bigelow", + "Drucker", + "Fisher", + "Meyer" ], - "joinedAuthorList": "Nicola J. Camp, Wei-Yu Lin, Alex Bigelow, George J. Burghel, Timothy L. Mosbruger, Marina A. Parry, Rosalie G. Waller, Sushilaben H. Rigas, Pei-Yi Tai, Kristofer Berrett, Venkatesh Rajamanickam, Rachel Cosby, Ian W. Brock, Brandt Jones, Dan Conneley, Robert Sargent, Guoying Wang, Rachel E. Factor, Philip S. Bernard, Lisa A. Cannon-Albright, Stacey Knight, Ryan Abo, Theresa Werner, Malcolm W. R. Reed, Jason Gertz, and Angela Cox" + "joinedAuthorList": "Alex Bigelow, Steven Drucker, Danyel Fisher, and Miriah Meyer", + "shortAuthorList": "Bigelow, Drucker, Fisher, and Meyer" }, "filename": "citation.bib", - "lastmod": "2020-09-27" - }, - "meta.json": { - "url": "/cv/publications/papers/2016_haplotype/meta.json", - "path": [ - "publications", - "papers", - "2016_haplotype" - ], - "name": "meta", - "extension": "json", - "contents": { - "hideInPrint": true - }, - "filename": "meta.json", - "lastmod": "2020-10-05" + "lastmod": "2022-08-27" } }, - "2019_vast_origraph": { - "talk.url": { - "url": "/cv/publications/papers/2019_vast_origraph/talk.url", - "path": [ - "publications", - "papers", - "2019_vast_origraph" - ], - "name": "talk", - "extension": "url", - "contents": "https://vimeo.com/372531346\n", - "filename": "talk.url", - "lastmod": "2020-10-23" - }, - "supplement.pdf": { - "url": "/cv/publications/papers/2019_vast_origraph/supplement.pdf", + "2016_hanpuku": { + "poster.pdf": { + "url": "/cv/publications/posters/2016_hanpuku/poster.pdf", "path": [ "publications", - "papers", - "2019_vast_origraph" + "posters", + "2016_hanpuku" ], - "name": "supplement", + "name": "poster", "extension": "pdf", - "filename": "supplement.pdf", + "filename": "poster.pdf", "lastmod": "2020-09-27" }, - "demo.url": { - "url": "/cv/publications/papers/2019_vast_origraph/demo.url", - "path": [ - "publications", - "papers", - "2019_vast_origraph" - ], - "name": "demo", - "extension": "url", - "contents": "https://youtu.be/bSFf2iD4TLI\n", - "filename": "demo.url", - "lastmod": "2020-12-04" - }, - "abstract.txt": { - "url": "/cv/publications/papers/2019_vast_origraph/abstract.txt", + "citation.bib": { + "url": "/cv/publications/posters/2016_hanpuku/citation.bib", "path": [ "publications", - "papers", - "2019_vast_origraph" + "posters", + "2016_hanpuku" ], - "name": "abstract", - "extension": "txt", - "contents": "Networks are a natural way of thinking about many datasets. The data on which a network is based, however, is rarely collected in a form that suits the analysis process, making it necessary to create and reshape networks. Data wrangling is widely acknowledged to be a critical part of the data analysis pipeline, yet interactive network wrangling has received little attention in the visualization research community. In this paper, we discuss a set of operations that are important for wrangling network datasets and introduce a visual data wrangling tool, Origraph, that enables analysts to apply these operations to their datasets. Key operations include creating a network from source data such as tables, reshaping a network by introducing new node or edge classes, filtering nodes or edges, and deriving new node or edge attributes. Our tool, Origraph, enables analysts to execute these operations with little to no programming, and to immediately visualize the results. Origraph provides views to investigate the network model, a sample of the network, and node and edge attributes. In addition, we introduce interfaces designed to aid analysts in specifying arguments for sensible network wrangling operations. We demonstrate the usefulness of Origraph in two Use Cases: first, we investigate gender bias in the film industry, and then the influence of money on the political support for the war in Yemen.\n", - "filename": "abstract.txt", - "lastmod": "2020-09-27" - }, - "publication.pdf": { - "url": "/cv/publications/papers/2019_vast_origraph/publication.pdf", + "name": "citation", + "extension": "bib", + "contents": { + "title": "Iterating Between Tools to Create and Edit Visualizations", + "author": "Bigelow, Alex and Drucker, Steven and Fisher, Danyel and Meyer, Miriah", + "howpublished": "University of Utah School of Computing Poster Competition", + "year": "2016", + "authorList": [ + "Alex Bigelow", + "Steven Drucker", + "Danyel Fisher", + "Miriah Meyer" + ], + "authorLastNames": [ + "Bigelow", + "Drucker", + "Fisher", + "Meyer" + ], + "joinedAuthorList": "Alex Bigelow, Steven Drucker, Danyel Fisher, and Miriah Meyer", + "shortAuthorList": "Bigelow, Drucker, Fisher, and Meyer" + }, + "filename": "citation.bib", + "lastmod": "2022-08-27" + } + }, + "2013_explosion": { + "poster.pdf": { + "url": "/cv/publications/posters/2013_explosion/poster.pdf", "path": [ "publications", - "papers", - "2019_vast_origraph" + "posters", + "2013_explosion" ], - "name": "publication", + "name": "poster", "extension": "pdf", - "filename": "publication.pdf", + "filename": "poster.pdf", "lastmod": "2020-09-27" }, - "description.html": { - "url": "/cv/publications/papers/2019_vast_origraph/description.html", + "award.txt": { + "url": "/cv/publications/posters/2013_explosion/award.txt", "path": [ "publications", - "papers", - "2019_vast_origraph" + "posters", + "2013_explosion" ], - "name": "description", - "extension": "html", - "filename": "description.html", + "name": "award", + "extension": "txt", + "contents": "Best Poster Award\n", + "filename": "award.txt", "lastmod": "2020-09-27" }, "citation.bib": { - "url": "/cv/publications/papers/2019_vast_origraph/citation.bib", + "url": "/cv/publications/posters/2013_explosion/citation.bib", "path": [ "publications", - "papers", - "2019_vast_origraph" + "posters", + "2013_explosion" ], "name": "citation", "extension": "bib", "contents": { - "title": "Origraph: Interactive Network Wrangling", - "author": "Bigelow, Alex and Nobre, Carolina and Meyer, Miriah and Lex, Alexander", - "booktitle": "2019 IEEE Conference on Visual Analytics Science and Technology (VAST)", - "pages": "81--92", - "year": "2019", - "organization": "IEEE", - "doi": "10.1109/VAST47406.2019.8986909", + "title": "Exploring the Biological Data Explosion", + "author": "Bigelow, Alex and Meyer, Miriah and Camp, Nicola J.", + "howpublished": "University of Utah School of Computing Poster Competition", + "year": "2013", "authorList": [ "Alex Bigelow", - "Carolina Nobre", "Miriah Meyer", - "Alexander Lex" + "Nicola J. Camp" ], - "joinedAuthorList": "Alex Bigelow, Carolina Nobre, Miriah Meyer, and Alexander Lex" + "authorLastNames": [ + "Bigelow", + "Meyer", + "Camp" + ], + "joinedAuthorList": "Alex Bigelow, Miriah Meyer, and Nicola J. Camp", + "shortAuthorList": "Bigelow, Meyer, and Camp" }, "filename": "citation.bib", - "lastmod": "2020-10-05" + "lastmod": "2020-09-27" + }, + "meta.json": { + "url": "/cv/publications/posters/2013_explosion/meta.json", + "path": [ + "publications", + "posters", + "2013_explosion" + ], + "name": "meta", + "extension": "json", + "contents": { + "award": "Best Poster Award" + }, + "filename": "meta.json", + "lastmod": "2020-09-27" } - }, - "2019_pacificvis_jacobs_ladder": { - "demo.url": { - "url": "/cv/publications/papers/2019_pacificvis_jacobs_ladder/demo.url", + } + }, + "papers": { + "2022_traveler": { + "publication.url": { + "url": "/cv/publications/papers/2022_traveler/publication.url", "path": [ "publications", "papers", - "2019_pacificvis_jacobs_ladder" + "2022_traveler" ], - "name": "demo", + "name": "publication", "extension": "url", - "contents": "https://youtu.be/2joyCdBSGKw\n", - "filename": "demo.url", - "lastmod": "2020-12-04" + "contents": "https://doi.org/10.1109/TVCG.2022.3209375", + "filename": "publication.url", + "lastmod": "2024-03-23" }, "abstract.txt": { - "url": "/cv/publications/papers/2019_pacificvis_jacobs_ladder/abstract.txt", + "url": "/cv/publications/papers/2022_traveler/abstract.txt", "path": [ "publications", "papers", - "2019_pacificvis_jacobs_ladder" + "2022_traveler" ], "name": "abstract", "extension": "txt", - "contents": "This paper reports on a simple visual technique that boils extracting a subgraph down to two operations—pivots and filters—that is agnostic to both the data abstraction, and its visual complexity scales independent of the size of the graph. The system’s design, as well as its qualitative evaluation with users, clarifies exactly when and how the user’s intent in a series of pivots is ambiguous—and, more usefully, when it is not. Reflections on our results show how, in the event of an ambiguous case, this innately practical operation could be further extended into “smart pivots” that anticipate the user’s intent beyond the current step. They also reveal ways that a series of graph pivots can expose the semantics of the data from the user’s perspective, and how this information could be leveraged to create adaptive data abstractions that do not rely as heavily on a system designer to create a comprehensive abstraction that anticipates all the user’s tasks.\n", + "contents": "Understanding the behavior of software in execution is a key step in identifying and fixing performance issues. This is especially important in high performance computing contexts where even minor performance tweaks can translate into large savings in terms of computational resource use. To aid performance analysis, developers may collect an execution trace - a chronological log of program activity during execution. As traces represent the full history, developers can discover a wide array of possibly previously unknown performance issues, making them an important artifact for exploratory performance analysis. However, interactive trace visualization is difficult due to issues of data size and complexity of meaning. Traces represent nanosecond-level events across many parallel processes, meaning the collected data is often large and difficult to explore. The rise of asynchronous task parallel programming paradigms complicates the relation between events and their probable cause. To address these challenges, we conduct a continuing design study in collaboration with high performance computing researchers. We develop diverse and hierarchical ways to navigate and represent execution trace data in support of their trace analysis tasks. Through an iterative design process, we developed Traveler, an integrated visualization platform for task parallel traces. Traveler provides multiple linked interfaces to help navigate trace data from multiple contexts. We evaluate the utility of Traveler through feedback from users and a case study, finding that integrating multiple modes of navigation in our design supported performance analysis tasks and led to the discovery of previously unknown behavior in a distributed array library.", "filename": "abstract.txt", - "lastmod": "2020-09-27" - }, - "publication.pdf": { - "url": "/cv/publications/papers/2019_pacificvis_jacobs_ladder/publication.pdf", - "path": [ - "publications", - "papers", - "2019_pacificvis_jacobs_ladder" - ], - "name": "publication", - "extension": "pdf", - "filename": "publication.pdf", - "lastmod": "2020-09-27" + "lastmod": "2022-08-27" }, "citation.bib": { - "url": "/cv/publications/papers/2019_pacificvis_jacobs_ladder/citation.bib", + "url": "/cv/publications/papers/2022_traveler/citation.bib", "path": [ "publications", "papers", - "2019_pacificvis_jacobs_ladder" + "2022_traveler" ], "name": "citation", "extension": "bib", "contents": { - "title": "Jacob's Ladder: The User Implications of Leveraging Graph Pivots", - "author": "Bigelow, Alex and Monroe, Megan", - "booktitle": "2019 IEEE Pacific Visualization Symposium (PacificVis)", - "pages": "47--54", - "year": "2019", - "organization": "IEEE", - "doi": "10.1109/PacificVis.2019.00014", + "author": "Sakin, Sayef Azad and Bigelow, Alex and Tohid, R. and Scully-Allison, Connor and Scheidegger, Carlos and Brandt, Steven R. and Taylor, Christopher and Huck, Kevin A. and Kaiser, Hartmut and Isaacs, Katherine E.", + "journal": "IEEE Transactions on Visualization and Computer Graphics", + "title": "Traveler: Navigating Task Parallel Traces for Performance Analysis", + "year": "2023", + "volume": "29", + "number": "1", + "pages": "788-797", + "keywords": "Task analysis;Performance analysis;Measurement;Data visualization;Codes;Navigation;High performance computing;software visualization;parallel computing;traces;performance analysis;event sequence visualization", + "doi": "10.1109/TVCG.2022.3209375", "authorList": [ + "Sayef Azad Sakin", "Alex Bigelow", - "Megan Monroe" + "R. Tohid", + "Connor Scully-Allison", + "Carlos Scheidegger", + "Steven R. Brandt", + "Christopher Taylor", + "Kevin A. Huck", + "Hartmut Kaiser", + "Katherine E. Isaacs" + ], + "authorLastNames": [ + "Sakin", + "Bigelow", + "Tohid", + "Scully-Allison", + "Scheidegger", + "Brandt", + "Taylor", + "Huck", + "Kaiser", + "Isaacs" ], - "joinedAuthorList": "Alex Bigelow and Megan Monroe" + "joinedAuthorList": "Sayef Azad Sakin, Alex Bigelow, R. Tohid, Connor Scully-Allison, Carlos Scheidegger, Steven R. Brandt, Christopher Taylor, Kevin A. Huck, Hartmut Kaiser, and Katherine E. Isaacs", + "shortAuthorList": "Sakin, Bigelow, Tohid, Scully-Allison, Scheidegger, Brandt, Taylor, Huck, Kaiser, and Isaacs" }, "filename": "citation.bib", - "lastmod": "2020-10-05" + "lastmod": "2022-08-27" } }, - "2020_ten_rules": { + "2023_chi_elephants": { "publication.url": { - "url": "/cv/publications/papers/2020_ten_rules/publication.url", + "url": "/cv/publications/papers/2023_chi_elephants/publication.url", "path": [ "publications", "papers", - "2020_ten_rules" + "2023_chi_elephants" ], "name": "publication", "extension": "url", - "contents": "https://doi.org/10.1371/journal.pcbi.1008226\n", + "contents": "https://doi.org/10.1145/3544548.3580669", "filename": "publication.url", - "lastmod": "2020-10-24" + "lastmod": "2024-03-23" }, - "citation.bib": { - "url": "/cv/publications/papers/2020_ten_rules/citation.bib", + "abstract.txt": { + "url": "/cv/publications/papers/2023_chi_elephants/abstract.txt", "path": [ "publications", "papers", - "2020_ten_rules" - ], - "name": "citation", - "extension": "bib", - "contents": { - "title": "Ten Simple Rules for Organizing a Data Science Workshop", - "volume": "16", - "issn": "1553-7358", - "url": "https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008226", - "doi": "10.1371/journal.pcbi.1008226", - "language": "en", - "number": "10", - "urldate": "2020-10-24", - "journal": "PLOS Computational Biology", - "author": "Ponsero, Alise and Bartelme, Ryan and Almeida, Gustavo de Oliveira and Bigelow, Alex and Tuteja, Reetu and Ellingson, Holly and Swetnam, Tyson and Merchant, Nirav and Oxnam, Maliaca and Lyons, Eric", - "month": "oct", - "year": "2020", - "note": "Publisher: Public Library of Science", - "keywords": "Computer software, Human learning, Instructors, Internet, Learning, Pedagogy, Reproducibility, Workshops", - "pages": "e1008226", - "authorList": [ - "Alise Ponsero", - "Ryan Bartelme", - "Gustavo de Oliveira Almeida", - "Alex Bigelow", - "Reetu Tuteja", - "Holly Ellingson", - "Tyson Swetnam", - "Nirav Merchant", - "Maliaca Oxnam", - "Eric Lyons" - ], - "joinedAuthorList": "Alise Ponsero, Ryan Bartelme, Gustavo de Oliveira Almeida, Alex Bigelow, Reetu Tuteja, Holly Ellingson, Tyson Swetnam, Nirav Merchant, Maliaca Oxnam, and Eric Lyons" - }, - "filename": "citation.bib", - "lastmod": "2020-10-24" - } - } - }, - "posters": { - "2015_hanpuku": { - "poster.pdf": { - "url": "/cv/publications/posters/2015_hanpuku/poster.pdf", - "path": [ - "publications", - "posters", - "2015_hanpuku" + "2023_chi_elephants" ], - "name": "poster", - "extension": "pdf", - "filename": "poster.pdf", - "lastmod": "2020-09-27" + "name": "abstract", + "extension": "txt", + "contents": "Two people looking at the same dataset will create different mental models, prioritize different attributes, and connect with different visualizations. We seek to understand the space of data abstractions associated with mental models and how well people communicate their mental models when sketching. Data abstractions have a profound influence on the visualization design, yet it’s unclear how universal they may be when not initially influenced by a representation. We conducted a study about how people create their mental models from a dataset. Rather than presenting tabular data, we presented each participant with one of three datasets in paragraph form, to avoid biasing the data abstraction and mental model. We observed various mental models, data abstractions, and depictions from the same dataset, and how these concepts are influenced by communication and purpose-seeking. Our results have implications for visualization design, especially during the discovery and data collection phase.", + "filename": "abstract.txt", + "lastmod": "2024-03-23" }, "citation.bib": { - "url": "/cv/publications/posters/2015_hanpuku/citation.bib", + "url": "/cv/publications/papers/2023_chi_elephants/citation.bib", "path": [ "publications", - "posters", - "2015_hanpuku" + "papers", + "2023_chi_elephants" ], "name": "citation", "extension": "bib", "contents": { - "title": "A Bridge Supporting Iteration Between Data Exploration and Data Storytelling", - "author": "Bigelow, Alex and Drucker, Steven and Fisher, Danyel and Meyer, Miriah", - "howpublished": "University of Utah School of Computing Poster Competition", - "year": "2015", + "author": "Williams, Katy and Bigelow, Alex and Isaacs, Katherine E.", + "title": "Data Abstraction Elephants: The Initial Diversity of Data Representations and Mental Models", + "year": "2023", + "isbn": "9781450394215", + "publisher": "Association for Computing Machinery", + "address": "New York, NY, USA", + "url": "https://doi.org/10.1145/3544548.3580669", + "doi": "10.1145/3544548.3580669", + "abstract": "Two people looking at the same dataset will create different mental models, prioritize different attributes, and connect with different visualizations. We seek to understand the space of data abstractions associated with mental models and how well people communicate their mental models when sketching. Data abstractions have a profound influence on the visualization design, yet it’s unclear how universal they may be when not initially influenced by a representation. We conducted a study about how people create their mental models from a dataset. Rather than presenting tabular data, we presented each participant with one of three datasets in paragraph form, to avoid biasing the data abstraction and mental model. We observed various mental models, data abstractions, and depictions from the same dataset, and how these concepts are influenced by communication and purpose-seeking. Our results have implications for visualization design, especially during the discovery and data collection phase.", + "booktitle": "Proceedings of the 2023 CHI Conference on Human Factors in Computing Systems", + "articleno": "803", + "numpages": "24", + "keywords": "Human-centered computing, data abstractions, visualization theory", + "location": ", Hamburg, Germany, ", + "series": "CHI '23", "authorList": [ + "Katy Williams", "Alex Bigelow", - "Steven Drucker", - "Danyel Fisher", - "Miriah Meyer" + "Katherine E. Isaacs" ], - "joinedAuthorList": "Alex Bigelow, Steven Drucker, Danyel Fisher, and Miriah Meyer" + "authorLastNames": [ + "Williams", + "Bigelow", + "Isaacs" + ], + "joinedAuthorList": "Katy Williams, Alex Bigelow, and Katherine E. Isaacs", + "shortAuthorList": "Williams, Bigelow, and Isaacs" }, "filename": "citation.bib", - "lastmod": "2020-09-27" + "lastmod": "2024-03-23" } }, - "2015_bob_ross": { - "poster.pdf": { - "url": "/cv/publications/posters/2015_bob_ross/poster.pdf", - "path": [ - "publications", - "posters", - "2015_bob_ross" - ], - "name": "poster", - "extension": "pdf", - "filename": "poster.pdf", - "lastmod": "2020-09-27" - }, - "publication.pdf": { - "url": "/cv/publications/posters/2015_bob_ross/publication.pdf", + "2014_targeted": { + "abstract.txt": { + "url": "/cv/publications/papers/2014_targeted/abstract.txt", "path": [ "publications", - "posters", - "2015_bob_ross" + "papers", + "2014_targeted" ], - "name": "publication", - "extension": "pdf", - "filename": "publication.pdf", - "lastmod": "2020-09-27" + "name": "abstract", + "extension": "txt", + "contents": "CASP8 at 2q33 is an established common, low risk susceptibility locus for breast cancer but functional variants are yet to be elucidated. Previously we used haplotype mining of 45 tSNPs in 3778 breast cancer cases and controls to identify a risk haplotype maximizing association evidence. A protective haplotype was also suggested. Here, we perform a focused sequencing study to identify the critical sequence variant/s.\n\nTo not exclude potential regulatory variants, we designed a custom Agilent SureSelect capture array to target all non-repetitive sequence in the 1 Mb region surrounding CASP8. The resulting 41 libraries for germline DNA (24 breast cancer cases homozygous for the risk haplotype, 17 cancer-free women carrying the protective haplotype) were sequenced on the Life Technologies SOLID system. A total of 1464 sequence variants were prioritized by their propensity to lie on the risk or protective haplotypes, resulting in the selection of 42 variants to follow-up with expression-QTL analysis (MAFs 0.1-0.4). Our RNA sequencing panel comprised 156 tissue samples from 88 women (68 breast tumor, 88 normal breast). Illumina TruSeq stranded mRNA sequencing was performed on an Illumina HiSeq 2000. Genotyping for the 42 selected variants was performed using Illumina BeadXpress. RNAseq eQTL analysis focused on 4 genes: CFLAR, CASP10, CASP8, ALS2CR12 using counts standardized to fragments per kilobase per million bases (FPKM). Differences in FPKM between carriers and non-carriers of the 42 DNA sequence variants were assessed in both normal and tumor tissues. Replication analyses were carried out on available TCGA data and published blood eQTL microarray data.\n\nIn normal tissue, an intronic variant in ALS2CR12 on the risk haplotype was best associated with CASP8 expression (19% decreased FPKM, p=9x10-5). Eight other variants (all in ALS2CR12 or CASP8) showed similar CASP8 decreases (p<10-3). Increased ALS2CR12 expression was also observed for the same variants, and decreased CASP8 expression was seen in tumor. Despite the difference in technologies, lower coverage and sparser genotyping, the decreased CASP8 and increased ALS2CR12 levels were replicated in both in the TCGA normal tissue (p=3x10-4) and blood eQTL data (p=4x10-14).\n\nIn tumor, our strongest eQTL results were for decreased expression of CFLAR (p=1x10-4) and CASP10 (p=4x10-5), identified for variants on the protective haplotype (including rs1045485). Examination of TCGA breast tumors did not replicate these findings; however read depths were substantially lower for these genes in the TCGA data.\n\nWe find evidence for two separate paths to 2q33 breast cancer risk. Reduction of CASP8 expression, which may lead to reduced apoptosis and an environment conducive to tumor development. Reduction of CFLAR-CASP10 expression in tumor may implicate autophagy leading to a challenging environment for tumors, but requires more replication.", + "filename": "abstract.txt", + "lastmod": "2022-08-27" }, "citation.bib": { - "url": "/cv/publications/posters/2015_bob_ross/citation.bib", + "url": "/cv/publications/papers/2014_targeted/citation.bib", "path": [ "publications", - "posters", - "2015_bob_ross" + "papers", + "2014_targeted" ], "name": "citation", "extension": "bib", "contents": { - "title": "Happy Accidents: Analyzing the Paintings of Bob Ross", - "author": "Warner, Ally and Dunstan, Jonathan and Bigelow, Alex", - "howpublished": "University of Utah Data Mining Class Project", - "year": "2015", + "title": "Targeted DNA and RNA sequencing identifies breast cancer risk variants associated with differential expression of CASP8 and CFLAR/CASP10", + "author": "Camp, Nicola J. and Lin, Wei-Yu and Bigelow, Alex and Parry, Marina A. and Mosbruger, Tim and Burghel, George and Rajamanickam, Venkatesh and Rigas, Sushilaben H. and Cosby, Rachel and Connley, Dan and Wang, Guoying and Tresa, George and Waller, Rosalie G. and Cannon-Albright, Lisa A. and Brandt, Jones and Sargent, Rob and Reed, Malcolm W. R. and Cox, Angela", + "journal": "Cancer Research", + "volume": "74", + "number": "19\\_Supplement", + "pages": "3267--3267", + "year": "2014", + "publisher": "AACR", "authorList": [ - "Ally Warner", - "Jonathan Dunstan", - "Alex Bigelow" + "Nicola J. Camp", + "Wei-Yu Lin", + "Alex Bigelow", + "Marina A. Parry", + "Tim Mosbruger", + "George Burghel", + "Venkatesh Rajamanickam", + "Sushilaben H. Rigas", + "Rachel Cosby", + "Dan Connley", + "Guoying Wang", + "George Tresa", + "Rosalie G. Waller", + "Lisa A. Cannon-Albright", + "Jones Brandt", + "Rob Sargent", + "Malcolm W. R. Reed", + "Angela Cox" + ], + "authorLastNames": [ + "Camp", + "Lin", + "Bigelow", + "Parry", + "Mosbruger", + "Burghel", + "Rajamanickam", + "Rigas", + "Cosby", + "Connley", + "Wang", + "Tresa", + "Waller", + "Cannon-Albright", + "Brandt", + "Sargent", + "Reed", + "Cox" ], - "joinedAuthorList": "Ally Warner, Jonathan Dunstan, and Alex Bigelow" + "joinedAuthorList": "Nicola J. Camp, Wei-Yu Lin, Alex Bigelow, Marina A. Parry, Tim Mosbruger, George Burghel, Venkatesh Rajamanickam, Sushilaben H. Rigas, Rachel Cosby, Dan Connley, Guoying Wang, George Tresa, Rosalie G. Waller, Lisa A. Cannon-Albright, Jones Brandt, Rob Sargent, Malcolm W. R. Reed, and Angela Cox", + "shortAuthorList": "Camp, Lin, Bigelow, Parry, Mosbruger, Burghel, Rajamanickam, Rigas, Cosby, Connley, Wang, Tresa, Waller, Cannon-Albright, Brandt, Sargent, Reed, and Cox" }, "filename": "citation.bib", - "lastmod": "2020-09-27" + "lastmod": "2022-08-27" } }, - "2016_hanpuku": { - "poster.pdf": { - "url": "/cv/publications/posters/2016_hanpuku/poster.pdf", + "2014_avi_reflections": { + "abstract.txt": { + "url": "/cv/publications/papers/2014_avi_reflections/abstract.txt", "path": [ "publications", - "posters", - "2016_hanpuku" - ], - "name": "poster", - "extension": "pdf", - "filename": "poster.pdf", + "papers", + "2014_avi_reflections" + ], + "name": "abstract", + "extension": "txt", + "contents": "In recent years many popular data visualizations have emerged that are created largely by designers whose main area of expertise is not computer science. Designers generate these visualizations using a handful of design tools and environments. To better inform the development of tools intended for designers working with data, we set out to understand designers’ challenges and perspectives. We interviewed professional designers, conducted observations of designers working with data in the lab, and observed designers working with data in team settings in the wild. A set of patterns emerged from these observations from which we extract a number of themes that provide a new perspective on design considerations for visualization tool creators, as well as on known engineering problems.\n", + "filename": "abstract.txt", "lastmod": "2020-09-27" }, - "citation.bib": { - "url": "/cv/publications/posters/2016_hanpuku/citation.bib", + "award.txt": { + "url": "/cv/publications/papers/2014_avi_reflections/award.txt", "path": [ "publications", - "posters", - "2016_hanpuku" + "papers", + "2014_avi_reflections" ], - "name": "citation", - "extension": "bib", - "contents": { - "title": "Iterating Between Tools to Create and Edit Visualizations", - "author": "Bigelow, Alex and Drucker, Steven and Fisher, Danyel and Meyer, Miriah", - "howpublished": "University of Utah School of Computing Poster Competition", - "year": "2016", - "authorList": [ - "Alex Bigelow", - "Steven Drucker", - "Danyel Fisher", - "Miriah Meyer" - ], - "joinedAuthorList": "Alex Bigelow, Steven Drucker, Danyel Fisher, and Miriah Meyer" - }, - "filename": "citation.bib", + "name": "award", + "extension": "txt", + "contents": "Best Paper Award\n", + "filename": "award.txt", "lastmod": "2020-09-27" - } - }, - "2014_reflections": { - "poster.pdf": { - "url": "/cv/publications/posters/2014_reflections/poster.pdf", + }, + "slides.url": { + "url": "/cv/publications/papers/2014_avi_reflections/slides.url", "path": [ "publications", - "posters", - "2014_reflections" + "papers", + "2014_avi_reflections" ], - "name": "poster", - "extension": "pdf", - "filename": "poster.pdf", + "name": "slides", + "extension": "url", + "contents": "http://sci.utah.edu/~vdl/papers/2014_avi_reflections_slides.pdf\n", + "filename": "slides.url", "lastmod": "2020-09-27" }, "citation.bib": { - "url": "/cv/publications/posters/2014_reflections/citation.bib", + "url": "/cv/publications/papers/2014_avi_reflections/citation.bib", "path": [ "publications", - "posters", - "2014_reflections" + "papers", + "2014_avi_reflections" ], "name": "citation", "extension": "bib", "contents": { - "title": "Reflections on How Designers Design With Data", + "title": "Reflections on How Designers Design with Data", "author": "Bigelow, Alex and Drucker, Steven and Fisher, Danyel and Meyer, Miriah", - "howpublished": "University of Utah School of Computing Poster Competition", + "booktitle": "Proceedings of the 2014 International Working Conference on Advanced Visual Interfaces", + "pages": "17--24", "year": "2014", + "organization": "ACM", + "doi": "10.1145/2598153.2598175", "authorList": [ "Alex Bigelow", "Steven Drucker", "Danyel Fisher", "Miriah Meyer" ], - "joinedAuthorList": "Alex Bigelow, Steven Drucker, Danyel Fisher, and Miriah Meyer" + "authorLastNames": [ + "Bigelow", + "Drucker", + "Fisher", + "Meyer" + ], + "joinedAuthorList": "Alex Bigelow, Steven Drucker, Danyel Fisher, and Miriah Meyer", + "shortAuthorList": "Bigelow, Drucker, Fisher, and Meyer" }, "filename": "citation.bib", + "lastmod": "2020-10-05" + }, + "supplement.zip": { + "url": "/cv/publications/papers/2014_avi_reflections/supplement.zip", + "path": [ + "publications", + "papers", + "2014_avi_reflections" + ], + "name": "supplement", + "extension": "zip", + "filename": "supplement.zip", "lastmod": "2020-09-27" }, - "award.txt": { - "url": "/cv/publications/posters/2014_reflections/award.txt", + "publication.pdf": { + "url": "/cv/publications/papers/2014_avi_reflections/publication.pdf", "path": [ "publications", - "posters", - "2014_reflections" + "papers", + "2014_avi_reflections" ], - "name": "award", - "extension": "txt", - "contents": "Best Poster Award\n", - "filename": "award.txt", + "name": "publication", + "extension": "pdf", + "filename": "publication.pdf", "lastmod": "2020-09-27" }, "meta.json": { - "url": "/cv/publications/posters/2014_reflections/meta.json", + "url": "/cv/publications/papers/2014_avi_reflections/meta.json", "path": [ "publications", - "posters", - "2014_reflections" + "papers", + "2014_avi_reflections" ], "name": "meta", "extension": "json", "contents": { - "award": "Best Poster Award" + "award": "Best Paper Award" }, "filename": "meta.json", "lastmod": "2020-09-27" } }, - "2013_explosion": { - "poster.pdf": { - "url": "/cv/publications/posters/2013_explosion/poster.pdf", + "2016_haplotype": { + "abstract.txt": { + "url": "/cv/publications/papers/2016_haplotype/abstract.txt", "path": [ "publications", - "posters", - "2013_explosion" + "papers", + "2016_haplotype" ], - "name": "poster", - "extension": "pdf", - "filename": "poster.pdf", + "name": "abstract", + "extension": "txt", + "contents": "The findings from genome-wide association studies hold enormous potential for novel insight into disease mechanisms. A major challenge in the field is to map these low-risk association signals to their underlying functional sequence variants(FSV). Simple sequence study designs are insufficient, as the vast numbers of statistically comparable variants and a limited knowledge of noncoding regulatory elements complicate prioritization. Furthermore, large sample sizes are typically required for adequate power to identify the initial association signals. One important question is whether similar sample sizes need to be sequenced to identify the FSVs. Here, we present a proof-of-principle example of an extreme discordant design to map FSVs within the 2q33 low-risk breast cancer locus. Our approach employed DNA sequencing of a small number of discordant haplotypes to efficiently identify candidate FSVs. Our results were consistent with those from a 2,000-fold larger, traditional imputation-based fine-mapping study. To prioritize further, we used expression-quantitative trait locus analysis of RNA sequencing from breast tissues, gene regulation annotations from the ENCODE consortium, and functional assays for differential enhancer activities. Notably, we implicate three regulatory variants at 2q33 that target CASP8 (rs3769823,rs3769821 in CASP8, and rs10197246 in ALS2CR12) as functionally relevant. We conclude that nested discordant haplotype sequencing is a promising approach to aid mapping of low-risk association loci. The ability to include more efficient sequencing designs into mapping efforts presents an opportunity for the field to capitalize on the potential of association loci and accelerate translation of association signals to their underlying FSVs.\n", + "filename": "abstract.txt", "lastmod": "2020-09-27" }, "citation.bib": { - "url": "/cv/publications/posters/2013_explosion/citation.bib", + "url": "/cv/publications/papers/2016_haplotype/citation.bib", "path": [ "publications", - "posters", - "2013_explosion" + "papers", + "2016_haplotype" ], "name": "citation", "extension": "bib", "contents": { - "title": "Exploring the Biological Data Explosion", - "author": "Bigelow, Alex and Meyer, Miriah and Camp, Nicola J.", - "howpublished": "University of Utah School of Computing Poster Competition", - "year": "2013", + "title": "Discordant Haplotype Sequencing Identifies Functional Variants at the 2q33 Breast Cancer Risk Locus", + "author": "Camp, Nicola J. and Lin, Wei-Yu and Bigelow, Alex and Burghel, George J. and Mosbruger, Timothy L. and Parry, Marina A. and Waller, Rosalie G. and Rigas, Sushilaben H. and Tai, Pei-Yi and Berrett, Kristofer and Rajamanickam, Venkatesh and Cosby, Rachel and Brock, Ian W. and Jones, Brandt and Conneley, Dan and Sargent, Robert and Wang, Guoying and Factor, Rachel E. and Bernard, Philip S. and Cannon-Albright, Lisa A. and Knight, Stacey and Abo, Ryan and Werner, Theresa and Reed, Malcolm W. R. and Gertz, Jason and Cox, Angela", + "journal": "Cancer research", + "volume": "76", + "number": "7", + "pages": "1916--1925", + "year": "2016", + "publisher": "AACR", "authorList": [ + "Nicola J. Camp", + "Wei-Yu Lin", "Alex Bigelow", - "Miriah Meyer", - "Nicola J. Camp" + "George J. Burghel", + "Timothy L. Mosbruger", + "Marina A. Parry", + "Rosalie G. Waller", + "Sushilaben H. Rigas", + "Pei-Yi Tai", + "Kristofer Berrett", + "Venkatesh Rajamanickam", + "Rachel Cosby", + "Ian W. Brock", + "Brandt Jones", + "Dan Conneley", + "Robert Sargent", + "Guoying Wang", + "Rachel E. Factor", + "Philip S. Bernard", + "Lisa A. Cannon-Albright", + "Stacey Knight", + "Ryan Abo", + "Theresa Werner", + "Malcolm W. R. Reed", + "Jason Gertz", + "Angela Cox" + ], + "authorLastNames": [ + "Camp", + "Lin", + "Bigelow", + "Burghel", + "Mosbruger", + "Parry", + "Waller", + "Rigas", + "Tai", + "Berrett", + "Rajamanickam", + "Cosby", + "Brock", + "Jones", + "Conneley", + "Sargent", + "Wang", + "Factor", + "Bernard", + "Cannon-Albright", + "Knight", + "Abo", + "Werner", + "Reed", + "Gertz", + "Cox" ], - "joinedAuthorList": "Alex Bigelow, Miriah Meyer, and Nicola J. Camp" + "joinedAuthorList": "Nicola J. Camp, Wei-Yu Lin, Alex Bigelow, George J. Burghel, Timothy L. Mosbruger, Marina A. Parry, Rosalie G. Waller, Sushilaben H. Rigas, Pei-Yi Tai, Kristofer Berrett, Venkatesh Rajamanickam, Rachel Cosby, Ian W. Brock, Brandt Jones, Dan Conneley, Robert Sargent, Guoying Wang, Rachel E. Factor, Philip S. Bernard, Lisa A. Cannon-Albright, Stacey Knight, Ryan Abo, Theresa Werner, Malcolm W. R. Reed, Jason Gertz, and Angela Cox", + "shortAuthorList": "Camp, Lin, Bigelow, Burghel, Mosbruger, Parry, Waller, Rigas, Tai, Berrett, Rajamanickam, Cosby, Brock, Jones, Conneley, Sargent, Wang, Factor, Bernard, Cannon-Albright, Knight, Abo, Werner, Reed, Gertz, and Cox" }, "filename": "citation.bib", - "lastmod": "2020-09-27" - }, - "award.txt": { - "url": "/cv/publications/posters/2013_explosion/award.txt", - "path": [ - "publications", - "posters", - "2013_explosion" - ], - "name": "award", - "extension": "txt", - "contents": "Best Poster Award\n", - "filename": "award.txt", - "lastmod": "2020-09-27" + "lastmod": "2022-08-27" }, "meta.json": { - "url": "/cv/publications/posters/2013_explosion/meta.json", + "url": "/cv/publications/papers/2016_haplotype/meta.json", "path": [ "publications", - "posters", - "2013_explosion" + "papers", + "2016_haplotype" ], "name": "meta", "extension": "json", "contents": { - "award": "Best Poster Award" + "hideInPrint": true }, "filename": "meta.json", - "lastmod": "2020-09-27" + "lastmod": "2020-10-05" } - } - }, - "theses": { - "2019_phd_dissertation": { + }, + "2019_infovis_atria": { "abstract.txt": { - "url": "/cv/publications/theses/2019_phd_dissertation/abstract.txt", + "url": "/cv/publications/papers/2019_infovis_atria/abstract.txt", "path": [ "publications", - "theses", - "2019_phd_dissertation" + "papers", + "2019_infovis_atria" ], "name": "abstract", "extension": "txt", - "contents": "Iteration is a ubiquitous need across many different visualization design workflows. For visual design, practitioners often need to transition between the automated generation of visuals and manual drawing; however, existing software makes free-form iteration between these modalities difficult or impossible. A similar challenge exists for data as well: data abstractions often need to be adjusted; however, many data reshaping operations— particularly graph wrangling operations—have support only in programming environments that may not be accessible to many visualization designers.\n\nThis dissertation begins with an effort to better understand how graphic designers, a specific subset of the broader visualization community, work with data. The lessons from that effort inspire our remaining contributions, which are directed toward the broader community of visualization practitioners: first, we present a software model and a system that make it possible to iterate between drawing and generative visualization. Second, we present a visual technique that enables inquiry into the relationship between two specific graph data wrangling operations: pivoting and filtering. Finally, we present an interface that supports a broader range of graph data wrangling operations that enable iteration between many different graph data abstractions.\n", + "contents": "Common pitfalls in visualization projects include lack of data availability and the domain users’ needs and focus changing too rapidly for the design process to complete. While it is often prudent to avoid such projects, we argue it can be beneficial to engage them in some cases as the visualization process can help refine data collection, solving a “chicken and egg” problem of having the data and tools to analyze it. We found this to be the case in the domain of task parallel computing where such data and tooling is an open area of research. Despite these hurdles, we conducted a design study. Through a tightly-coupled iterative design process, we built Atria, a multi-view execution graph visualization to support performance analysis. Atria simplifies the initial representation of the execution graph by aggregating nodes as related to their line of code. We deployed Atria on multiple platforms, some requiring design alteration. We describe how we adapted the design study methodology to the “moving target” of both the data and the domain experts’ concerns and how this movement kept both the visualization and programming project healthy. We reflect on our process and discuss what factors allow the project to be successful in the presence of changing data and user needs.\n", "filename": "abstract.txt", "lastmod": "2020-09-27" }, - "publication.pdf": { - "url": "/cv/publications/theses/2019_phd_dissertation/publication.pdf", - "path": [ - "publications", - "theses", - "2019_phd_dissertation" - ], - "name": "publication", - "extension": "pdf", - "filename": "publication.pdf", - "lastmod": "2020-09-27" - }, "citation.bib": { - "url": "/cv/publications/theses/2019_phd_dissertation/citation.bib", + "url": "/cv/publications/papers/2019_infovis_atria/citation.bib", "path": [ "publications", - "theses", - "2019_phd_dissertation" + "papers", + "2019_infovis_atria" ], "name": "citation", "extension": "bib", "contents": { - "title": "Reflections, Models, and Software for Iterative Visualization Design", - "author": "Bigelow, Alex", - "school": "University of Utah", + "title": "Visualizing a Moving Target: A Design Study on Task Parallel Programs in the Presence of Evolving Data and Concerns", + "author": "Williams, Katy and Bigelow, Alex and Isaacs, Katherine E.", + "journal": "IEEE Transactions on Visualization and Computer Graphics", + "volume": "26", + "number": "1", + "pages": "1118--1128", "year": "2019", + "publisher": "IEEE", + "doi": "10.1109/TVCG.2019.2934285", "authorList": [ - "Alex Bigelow" + "Katy Williams", + "Alex Bigelow", + "Katherine E. Isaacs" ], - "joinedAuthorList": "Alex Bigelow", - "howpublished": "University of Utah PhD Dissertation" + "authorLastNames": [ + "Williams", + "Bigelow", + "Isaacs" + ], + "joinedAuthorList": "Katy Williams, Alex Bigelow, and Katherine E. Isaacs", + "shortAuthorList": "Williams, Bigelow, and Isaacs" }, "filename": "citation.bib", - "lastmod": "2020-09-27" - } - }, - "2012_bs_thesis": { - "abstract.txt": { - "url": "/cv/publications/theses/2012_bs_thesis/abstract.txt", + "lastmod": "2022-08-27" + }, + "talk.url": { + "url": "/cv/publications/papers/2019_infovis_atria/talk.url", "path": [ "publications", - "theses", - "2012_bs_thesis" + "papers", + "2019_infovis_atria" ], - "name": "abstract", - "extension": "txt", - "contents": "Some misunderstanding is inevitable in any interdisciplinary work, and recognizing and handling misunderstanding quickly is vital to the success of a collaboration. Many misunderstandings arise from what appears to be common knowledge to a domain scientist, but is not something that a computer scientist would think to ask about. The use of experimental visualization as an inter-collaboration communication tool can highlight these important misunderstandings that would otherwise severely impair the collaboration.\n\nVisualization itself, however, is a powerful tool; if used carefully it can open doors to understanding and discovery, but it can also control, warp, or even limit how a visualization designer (and consequently a scientist) thinks about a problem. A willingness to abandon erroneous designs and even systems, regardless of the effort involved in creating and understanding them, is also very important for such a collaboration.\n\nThis case study of data exploration via experimental visualization is in the space of next-generation sequencing data. For most of the history of genetics, the main bottleneck in the rate of discovery has been the difficulty in obtaining data. Next generation sequencing is a relatively new technology that allows biologists a way to obtain genetic data at a fraction of the cost and unprecedented speeds compared to conventional sequencing. With the advent of NGS data, the bottleneck has shifted from the burden of data acquisition to the analysis of huge amounts of data.\n", - "filename": "abstract.txt", - "lastmod": "2020-09-27" + "name": "talk", + "extension": "url", + "contents": "https://vimeo.com/370668837\n", + "filename": "talk.url", + "lastmod": "2020-10-23" }, "publication.pdf": { - "url": "/cv/publications/theses/2012_bs_thesis/publication.pdf", + "url": "/cv/publications/papers/2019_infovis_atria/publication.pdf", "path": [ "publications", - "theses", - "2012_bs_thesis" + "papers", + "2019_infovis_atria" ], "name": "publication", "extension": "pdf", "filename": "publication.pdf", "lastmod": "2020-09-27" - }, - "citation.bib": { - "url": "/cv/publications/theses/2012_bs_thesis/citation.bib", + } + }, + "2020_guidelines": { + "results.url": { + "url": "/cv/publications/papers/2020_guidelines/results.url", "path": [ "publications", - "theses", - "2012_bs_thesis" + "papers", + "2020_guidelines" ], - "name": "citation", - "extension": "bib", - "contents": { - "title": "Driving Genetics With Experimental Visualization", - "author": "Bigelow, Alex", - "school": "University of Utah", - "year": "2012", - "authorList": [ - "Alex Bigelow" - ], - "joinedAuthorList": "Alex Bigelow", - "howpublished": "University of Utah Thesis" - }, - "filename": "citation.bib", - "lastmod": "2020-09-27" - } - } - }, - "abstracts": { - "2020_pearc": { + "name": "results", + "extension": "url", + "contents": "https://alex-r-bigelow.github.io/wrangling-survey/Responses.html\n", + "filename": "results.url", + "lastmod": "2020-10-23" + }, "abstract.txt": { - "url": "/cv/publications/abstracts/2020_pearc/abstract.txt", + "url": "/cv/publications/papers/2020_guidelines/abstract.txt", "path": [ "publications", - "abstracts", - "2020_pearc" + "papers", + "2020_guidelines" ], "name": "abstract", "extension": "txt", - "contents": "We describe an interactive computing environment called JetLag. JetLag implements the following features of Phylanx project: (1) Phylanx, a Python-based asynchronous array computing toolkit; (2) the APEX performance measurement library; (3) a performance visualization framework called Traveler; (4) the Tapis/Agave Science as a Service middleware; and (6) a container infrastructure that includes Docker-based Jupyter notebook for the client and a singularity image for the server. The running system starts with a user performing array computations on their workstation or laptop. If, at some point, the calculation the user is performing becomes sufficiently intensive or numerous, it can be packaged and sent to another machine where it will run (through the batch queue system if there is one), produce a result, and have that result sent back to the user’s local interface. Whether the calculation is local or remote, the user will be able to use APEX and Traveler to diagnose and fix performance related problems. The JetLag system is suitable for a variety of array computational tasks, including machine learning and exploratory data analysis.\n", + "contents": "Many data abstraction types, such as networks or set relationships, remain unfamiliar to data workers beyond the\nvisualization research community. We conduct a survey and series of interviews about how people describe their data, either directly or\nindirectly. We refer to the latter as latent data abstractions. We conduct a Grounded Theory analysis that (1) interprets the extent to\nwhich latent data abstractions exist, (2) reveals the far-reaching effects that the interventionist pursuit of such abstractions can have on\ndata workers, (3) describes why and when data workers may resist such explorations, and (4) suggests how to take advantage of\nopportunities and mitigate risks through transparency about visualization research perspectives and agendas. We then use the themes\nand codes discovered in the Grounded Theory analysis to develop guidelines for data abstraction in visualization projects. To continue\nthe discussion, we make our dataset open along with a visual interface for further exploration.\n", "filename": "abstract.txt", "lastmod": "2020-10-05" }, - "publication.pdf": { - "url": "/cv/publications/abstracts/2020_pearc/publication.pdf", - "path": [ - "publications", - "abstracts", - "2020_pearc" - ], - "name": "publication", - "extension": "pdf", - "filename": "publication.pdf", - "lastmod": "2020-10-05" - }, "citation.bib": { - "url": "/cv/publications/abstracts/2020_pearc/citation.bib", + "url": "/cv/publications/papers/2020_guidelines/citation.bib", "path": [ "publications", - "abstracts", - "2020_pearc" + "papers", + "2020_guidelines" ], "name": "citation", "extension": "bib", "contents": { - "author": "Brandt, Steven R. and Bigelow, Alex and Sakin, Sayef Azad and Williams, Katy and Isaacs, Katherine E. and Huck, Kevin and Tohid, Rod and Wagle, Bibek and Shirzad, Shahrzad and Kaiser, Hartmut", - "title": "JetLag: An Interactive, Asynchronous Array Computing Environment", + "title": "Guidelines For Pursuing and Revealing Data Abstractions", + "author": "Bigelow, Alex and Williams, Katy and Isaacs, Katherine E.", + "journal": "IEEE Transactions on Visualization and Computer Graphics", "year": "2020", - "isbn": "9781450366892", - "publisher": "Association for Computing Machinery", - "address": "New York, NY, USA", - "url": "https://doi.org/10.1145/3311790.3396657", - "doi": "10.1145/3311790.3396657", - "abstract": "We describe an interactive computing environment called JetLag. JetLag implements the following features of Phylanx project: (1) Phylanx, a Python-based asynchronous array computing toolkit; (2) the APEX performance measurement library; (3) a performance visualization framework called Traveler; (4) the Tapis/Agave Science as a Service middleware; and (6) a container infrastructure that includes Docker-based Jupyter notebook for the client and a singularity image for the server. The running system starts with a user performing array computations on their workstation or laptop. If, at some point, the calculation the user is performing becomes sufficiently intensive or numerous, it can be packaged and sent to another machine where it will run (through the batch queue system if there is one), produce a result, and have that result sent back to the user’s local interface. Whether the calculation is local or remote, the user will be able to use APEX and Traveler to diagnose and fix performance related problems. The JetLag system is suitable for a variety of array computational tasks, including machine learning and exploratory data analysis. ", - "booktitle": "Practice and Experience in Advanced Research Computing", - "pages": "8–12", - "numpages": "5", - "keywords": "performance visualization, interactive computing, research environment, asynchronous, cloud computing, performance tuning, array", - "location": "Portland, OR, USA", - "series": "PEARC '20", + "publisher": "IEEE", "authorList": [ - "Steven R. Brandt", "Alex Bigelow", - "Sayef Azad Sakin", "Katy Williams", - "Katherine E. Isaacs", - "Kevin Huck", - "Rod Tohid", - "Bibek Wagle", - "Shahrzad Shirzad", - "Hartmut Kaiser" + "Katherine E. Isaacs" ], - "joinedAuthorList": "Steven R. Brandt, Alex Bigelow, Sayef Azad Sakin, Katy Williams, Katherine E. Isaacs, Kevin Huck, Rod Tohid, Bibek Wagle, Shahrzad Shirzad, and Hartmut Kaiser" + "authorLastNames": [ + "Bigelow", + "Williams", + "Isaacs" + ], + "joinedAuthorList": "Alex Bigelow, Katy Williams, and Katherine E. Isaacs", + "shortAuthorList": "Bigelow, Williams, and Isaacs" }, "filename": "citation.bib", - "lastmod": "2020-10-05" - } - }, - "2013_compariseq": { - "poster.pdf": { - "url": "/cv/publications/abstracts/2013_compariseq/poster.pdf", + "lastmod": "2022-08-27" + }, + "talk.url": { + "url": "/cv/publications/papers/2020_guidelines/talk.url", "path": [ "publications", - "abstracts", - "2013_compariseq" + "papers", + "2020_guidelines" ], - "name": "poster", - "extension": "pdf", - "filename": "poster.pdf", - "lastmod": "2020-09-27" + "name": "talk", + "extension": "url", + "contents": "https://youtu.be/DhPiHvtgtTI\n", + "filename": "talk.url", + "lastmod": "2020-10-23" }, "publication.pdf": { - "url": "/cv/publications/abstracts/2013_compariseq/publication.pdf", + "url": "/cv/publications/papers/2020_guidelines/publication.pdf", "path": [ "publications", - "abstracts", - "2013_compariseq" + "papers", + "2020_guidelines" ], "name": "publication", "extension": "pdf", "filename": "publication.pdf", - "lastmod": "2020-09-27" - }, - "citation.bib": { - "url": "/cv/publications/abstracts/2013_compariseq/citation.bib", - "path": [ - "publications", - "abstracts", - "2013_compariseq" - ], - "name": "citation", - "extension": "bib", - "contents": { - "title": "compariSeq: Rethinking Sequence Logos", - "author": "McKenna, Sean and Quinan, Philip S. and Bigelow, Alex", - "year": "2013", - "booktitle": "Proceedings of the 5th Symposium on Biological Data Visualization (BioVis'13)", - "authorList": [ - "Sean McKenna", - "Philip S. Quinan", - "Alex Bigelow" - ], - "joinedAuthorList": "Sean McKenna, Philip S. Quinan, and Alex Bigelow" - }, - "filename": "citation.bib", - "lastmod": "2020-09-27" + "lastmod": "2020-10-05" }, - "compariSeq.png": { - "url": "/cv/publications/abstracts/2013_compariseq/compariSeq.png", + "osf.url": { + "url": "/cv/publications/papers/2020_guidelines/osf.url", "path": [ "publications", - "abstracts", - "2013_compariseq" + "papers", + "2020_guidelines" ], - "name": "compariSeq", - "extension": "png", - "filename": "compariSeq.png", - "lastmod": "2020-09-27" + "name": "osf", + "extension": "url", + "contents": "https://osf.io/s2wmp/\n", + "filename": "osf.url", + "lastmod": "2020-10-23" } }, - "2018_murejs": { - "poster.svg": { - "url": "/cv/publications/abstracts/2018_murejs/poster.svg", + "2016_infovis_hanpuku": { + "demo.url": { + "url": "/cv/publications/papers/2016_infovis_hanpuku/demo.url", "path": [ "publications", - "abstracts", - "2018_murejs" + "papers", + "2016_infovis_hanpuku" ], - "name": "poster", - "extension": "svg", - "filename": "poster.svg", - "lastmod": "2020-09-27" + "name": "demo", + "extension": "url", + "contents": "https://youtu.be/eNoDZcs7vVs\n", + "filename": "demo.url", + "lastmod": "2020-12-04" }, - "poster.pdf": { - "url": "/cv/publications/abstracts/2018_murejs/poster.pdf", + "abstract.txt": { + "url": "/cv/publications/papers/2016_infovis_hanpuku/abstract.txt", "path": [ "publications", - "abstracts", - "2018_murejs" + "papers", + "2016_infovis_hanpuku" ], - "name": "poster", - "extension": "pdf", - "filename": "poster.pdf", + "name": "abstract", + "extension": "txt", + "contents": "A common workflow for visualization designers begins with a generative tool, like D3 or Processing, to create the initial visualization; and proceeds to a drawing tool, like Adobe Illustrator or Inkscape, for editing and cleaning. Unfortunately, this is typically a one-way process: once a visualization is exported from the generative tool into a drawing tool, it is difficult to make further, data-driven changes. In this paper, we propose a bridge model to allow designers to bring their work back from the drawing tool to re-edit in the generative tool. Our key insight is to recast this iteration challenge as a merge problem - similar to when two people are editing a document and changes between them need to reconciled. We also present a specific instantiation of this model, a tool called Hanpuku, which bridges between D3 scripts and Illustrator. We show several examples of visualizations that are iteratively created using Hanpuku in order to illustrate the flexibility of the approach. We further describe several hypothetical tools that bridge between other visualization tools to emphasize the generality of the model.\n", + "filename": "abstract.txt", "lastmod": "2020-09-27" }, - "abstract.txt": { - "url": "/cv/publications/abstracts/2018_murejs/abstract.txt", + "fastForward.mp4": { + "url": "/cv/publications/papers/2016_infovis_hanpuku/fastForward.mp4", "path": [ "publications", - "abstracts", - "2018_murejs" + "papers", + "2016_infovis_hanpuku" ], - "name": "abstract", - "extension": "txt", - "contents": "When interpreting data as a graph for visualization, an analyst first assigns semantic meaning to graph concepts. For example, they may choose to represent actors and movies as nodes, and roles as edges. Alternatively, they may wish to represent movies as edges, connecting actor nodes when they collaborate. Data abstraction choices such as these are critical, because different data abstractions can limit—or inspire—different analysis questions, approaches, perspectives, and visualizations.\n\nHowever, current network modeling frameworks, systems, and databases narrowly define graph abstraction constructs—such as nodes, edges, node / edge classes, supernodes, hyperedges, etc.—in terms of how the data is stored in memory or on disk, rather than semantic, human-driven abstractions. Consequently, the ability of an analyst to iterate on a data abstraction becomes fundamentally limited by the implementation details of data wrangling software.\n\nWe present work-in-progress toward a broader framework for modeling network data that is less dependent on its underlying structure and storage. Our goal is to use semantic data abstraction constructs to inform how algorithms wrangle data, instead of allowing algorithmic concerns to define and constrain the semantics.\n\nWe also present mure.js, a software library that represents an initial implementation of this framework, allowing users to map semantic graph constructs to arbitrary data structures as metadata, that can, in turn, be used to select, navigate, and reshape the under- lying data. Additionally, we discuss an early software prototype of a visual graph wrangling system based on this library.\n", - "filename": "abstract.txt", + "name": "fastForward", + "extension": "mp4", + "filename": "fastForward.mp4", "lastmod": "2020-09-27" }, - "publication.pdf": { - "url": "/cv/publications/abstracts/2018_murejs/publication.pdf", + "slides.url": { + "url": "/cv/publications/papers/2016_infovis_hanpuku/slides.url", "path": [ "publications", - "abstracts", - "2018_murejs" + "papers", + "2016_infovis_hanpuku" ], - "name": "publication", - "extension": "pdf", - "filename": "publication.pdf", + "name": "slides", + "extension": "url", + "contents": "http://www.cs.utah.edu/~abigelow/Downloads/papers/VisInPractice2016.key\n", + "filename": "slides.url", "lastmod": "2020-09-27" }, "citation.bib": { - "url": "/cv/publications/abstracts/2018_murejs/citation.bib", + "url": "/cv/publications/papers/2016_infovis_hanpuku/citation.bib", "path": [ "publications", - "abstracts", - "2018_murejs" + "papers", + "2016_infovis_hanpuku" ], "name": "citation", "extension": "bib", "contents": { - "title": "Mure. js: Toward Flexible Authoring and Reshaping of Networks", - "author": "Bigelow, Alex and Nobre, Carolina and Lex, Alexander and Meyer, Miriah", - "year": "2018", - "booktitle": "Proceedings of the IEEE Information Visualization Conference-Posters (InfoVis'18)", + "title": "Iterating Between Tools to Create and Edit Visualizations", + "author": "Bigelow, Alex and Drucker, Steven and Fisher, Danyel and Meyer, Miriah", + "journal": "IEEE Transactions on Visualization and Computer Graphics", + "volume": "23", + "number": "1", + "pages": "481--490", + "year": "2016", + "publisher": "IEEE", + "doi": "10.1109/TVCG.2016.2598609", "authorList": [ "Alex Bigelow", - "Carolina Nobre", - "Alexander Lex", + "Steven Drucker", + "Danyel Fisher", "Miriah Meyer" ], - "joinedAuthorList": "Alex Bigelow, Carolina Nobre, Alexander Lex, and Miriah Meyer" + "authorLastNames": [ + "Bigelow", + "Drucker", + "Fisher", + "Meyer" + ], + "joinedAuthorList": "Alex Bigelow, Steven Drucker, Danyel Fisher, and Miriah Meyer", + "shortAuthorList": "Bigelow, Drucker, Fisher, and Meyer" }, "filename": "citation.bib", + "lastmod": "2020-10-05" + }, + "supplement.zip": { + "url": "/cv/publications/papers/2016_infovis_hanpuku/supplement.zip", + "path": [ + "publications", + "papers", + "2016_infovis_hanpuku" + ], + "name": "supplement", + "extension": "zip", + "filename": "supplement.zip", "lastmod": "2020-09-27" }, - "fastForward.mp4": { - "url": "/cv/publications/abstracts/2018_murejs/fastForward.mp4", + "talk.url": { + "url": "/cv/publications/papers/2016_infovis_hanpuku/talk.url", "path": [ "publications", - "abstracts", - "2018_murejs" + "papers", + "2016_infovis_hanpuku" ], - "name": "fastForward", - "extension": "mp4", - "filename": "fastForward.mp4", + "name": "talk", + "extension": "url", + "contents": "https://vimeo.com/201779979\n", + "filename": "talk.url", + "lastmod": "2020-10-23" + }, + "publication.pdf": { + "url": "/cv/publications/papers/2016_infovis_hanpuku/publication.pdf", + "path": [ + "publications", + "papers", + "2016_infovis_hanpuku" + ], + "name": "publication", + "extension": "pdf", + "filename": "publication.pdf", "lastmod": "2020-09-27" } }, - "2016_vip_resonant_lab": { - "slides.url": { - "url": "/cv/publications/abstracts/2016_vip_resonant_lab/slides.url", + "2019_pacificvis_jacobs_ladder": { + "demo.url": { + "url": "/cv/publications/papers/2019_pacificvis_jacobs_ladder/demo.url", "path": [ "publications", - "abstracts", - "2016_vip_resonant_lab" + "papers", + "2019_pacificvis_jacobs_ladder" ], - "name": "slides", + "name": "demo", "extension": "url", - "contents": "http://www.cs.utah.edu/~abigelow/Downloads/papers/VisInPractice2016.key\n", - "filename": "slides.url", - "lastmod": "2020-09-27" + "contents": "https://youtu.be/2joyCdBSGKw\n", + "filename": "demo.url", + "lastmod": "2020-12-04" }, "abstract.txt": { - "url": "/cv/publications/abstracts/2016_vip_resonant_lab/abstract.txt", + "url": "/cv/publications/papers/2019_pacificvis_jacobs_ladder/abstract.txt", "path": [ "publications", - "abstracts", - "2016_vip_resonant_lab" + "papers", + "2019_pacificvis_jacobs_ladder" ], "name": "abstract", "extension": "txt", - "contents": "Visualization practitioners are constantly developing new, innovative ways to visualize data, but much of the software that practitioners produce does not make it into production in professional systems. To solve this problem, we have developed and informally tested two open source systems. The first, Candela, is a framework and API for creating visualization components for the web that can wrap up new or existing visualizations as needed. Because Candela’s API generalizes the inputs to a visualization, we have also developed a system called Resonant Laboratory that makes it possible for novice users to connect arbitrary datasets to Candela visualizations. Together, these systems enable novice users to explore and share their data with the growing library of state-of-the-art visualization techniques.\n", + "contents": "This paper reports on a simple visual technique that boils extracting a subgraph down to two operations—pivots and filters—that is agnostic to both the data abstraction, and its visual complexity scales independent of the size of the graph. The system’s design, as well as its qualitative evaluation with users, clarifies exactly when and how the user’s intent in a series of pivots is ambiguous—and, more usefully, when it is not. Reflections on our results show how, in the event of an ambiguous case, this innately practical operation could be further extended into “smart pivots” that anticipate the user’s intent beyond the current step. They also reveal ways that a series of graph pivots can expose the semantics of the data from the user’s perspective, and how this information could be leveraged to create adaptive data abstractions that do not rely as heavily on a system designer to create a comprehensive abstraction that anticipates all the user’s tasks.\n", "filename": "abstract.txt", "lastmod": "2020-09-27" }, - "publication.pdf": { - "url": "/cv/publications/abstracts/2016_vip_resonant_lab/publication.pdf", - "path": [ - "publications", - "abstracts", - "2016_vip_resonant_lab" - ], - "name": "publication", - "extension": "pdf", - "filename": "publication.pdf", - "lastmod": "2020-09-27" - }, "citation.bib": { - "url": "/cv/publications/abstracts/2016_vip_resonant_lab/citation.bib", + "url": "/cv/publications/papers/2019_pacificvis_jacobs_ladder/citation.bib", "path": [ "publications", - "abstracts", - "2016_vip_resonant_lab" + "papers", + "2019_pacificvis_jacobs_ladder" ], "name": "citation", "extension": "bib", "contents": { - "title": "Resonant Laboratory and Candela: Spreading Your Visualization Ideas to the Masses", - "author": "Bigelow, Alex and Choudhury, Roni and Baumes, Jeffrey", - "booktitle": "Proceedings of the Workshop on Visualization in Practice (VIP'16)", - "year": "2016", + "title": "Jacob's Ladder: The User Implications of Leveraging Graph Pivots", + "author": "Bigelow, Alex and Monroe, Megan", + "booktitle": "2019 IEEE Pacific Visualization Symposium (PacificVis)", + "pages": "47--54", + "year": "2019", + "organization": "IEEE", + "doi": "10.1109/PacificVis.2019.00014", "authorList": [ "Alex Bigelow", - "Roni Choudhury", - "Jeffrey Baumes" + "Megan Monroe" ], - "joinedAuthorList": "Alex Bigelow, Roni Choudhury, and Jeffrey Baumes" + "authorLastNames": [ + "Bigelow", + "Monroe" + ], + "joinedAuthorList": "Alex Bigelow and Megan Monroe", + "shortAuthorList": "Bigelow and Monroe" }, "filename": "citation.bib", - "lastmod": "2020-09-27" - }, - "award.txt": { - "url": "/cv/publications/abstracts/2016_vip_resonant_lab/award.txt", - "path": [ - "publications", - "abstracts", - "2016_vip_resonant_lab" - ], - "name": "award", - "extension": "txt", - "contents": "Best Paper Award\n", - "filename": "award.txt", - "lastmod": "2020-09-27" + "lastmod": "2020-10-05" }, - "meta.json": { - "url": "/cv/publications/abstracts/2016_vip_resonant_lab/meta.json", + "publication.pdf": { + "url": "/cv/publications/papers/2019_pacificvis_jacobs_ladder/publication.pdf", "path": [ "publications", - "abstracts", - "2016_vip_resonant_lab" + "papers", + "2019_pacificvis_jacobs_ladder" ], - "name": "meta", - "extension": "json", - "contents": { - "award": "Best Paper Award" - }, - "filename": "meta.json", + "name": "publication", + "extension": "pdf", + "filename": "publication.pdf", "lastmod": "2020-09-27" } }, - "2020_pyhpc": { - "abstract.txt": { - "url": "/cv/publications/abstracts/2020_pyhpc/abstract.txt", + "2020_ten_rules": { + "publication.url": { + "url": "/cv/publications/papers/2020_ten_rules/publication.url", "path": [ "publications", - "abstracts", - "2020_pyhpc" + "papers", + "2020_ten_rules" ], - "name": "abstract", - "extension": "txt", - "contents": "We describe JetLag, a Python-based environment that provides access to a distributed, interactive, asynchronous many-task (AMT) computing framework called Phylanx. This environment encompasses the entire computing process, from a Jupyter front-end for managing code and results to the collection and visualization of performance data.\n\nWe use a Python decorator to access the abstract syntax tree of Python functions and transpile them into a set of C++ data structures which are then executed by the HPX runtime. The environment includes services for sending functions and their arguments to run as jobs on remote resources.\n\nA set of Docker and Singularity containers are used to simplify the setup of the JetLag environment. The JetLag system is suitable for a variety of array computational tasks, including machine learning and exploratory data analysis.\n", - "filename": "abstract.txt", - "lastmod": "2020-10-16" + "name": "publication", + "extension": "url", + "contents": "https://doi.org/10.1371/journal.pcbi.1008226\n", + "filename": "publication.url", + "lastmod": "2020-10-24" }, "citation.bib": { - "url": "/cv/publications/abstracts/2020_pyhpc/citation.bib", + "url": "/cv/publications/papers/2020_ten_rules/citation.bib", "path": [ "publications", - "abstracts", - "2020_pyhpc" + "papers", + "2020_ten_rules" ], "name": "citation", "extension": "bib", "contents": { - "author": "Brandt, Steven R. and Hasheminezhad, Bita and Wu, Nanmiao and Sakin, Sayef Azad and Bigelow, Alex R. and Isaacs, Katherine E. and Huck, Kevin and Kaiser, Hartmut", - "booktitle": "2020 IEEE/ACM 9th Workshop on Python for High-Performance and Scientific Computing (PyHPC)", - "title": "Distributed Asynchronous Array Computing with the JetLag Environment", + "title": "Ten Simple Rules for Organizing a Data Science Workshop", + "volume": "16", + "issn": "1553-7358", + "url": "https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008226", + "doi": "10.1371/journal.pcbi.1008226", + "language": "en", + "number": "10", + "urldate": "2020-10-24", + "journal": "PLOS Computational Biology", + "author": "Ponsero, Alise and Bartelme, Ryan and Almeida, Gustavo de Oliveira and Bigelow, Alex and Tuteja, Reetu and Ellingson, Holly and Swetnam, Tyson and Merchant, Nirav and Oxnam, Maliaca and Lyons, Eric", + "month": "oct", "year": "2020", - "volume": "", - "number": "", - "pages": "49-57", - "doi": "10.1109/PyHPC51966.2020.00011", + "note": "Publisher: Public Library of Science", + "keywords": "Computer software, Human learning, Instructors, Internet, Learning, Pedagogy, Reproducibility, Workshops", + "pages": "e1008226", "authorList": [ - "Steven R. Brandt", - "Bita Hasheminezhad", - "Nanmiao Wu", - "Sayef Azad Sakin", - "Alex R. Bigelow", - "Katherine E. Isaacs", - "Kevin Huck", - "Hartmut Kaiser" + "Alise Ponsero", + "Ryan Bartelme", + "Gustavo de Oliveira Almeida", + "Alex Bigelow", + "Reetu Tuteja", + "Holly Ellingson", + "Tyson Swetnam", + "Nirav Merchant", + "Maliaca Oxnam", + "Eric Lyons" + ], + "authorLastNames": [ + "Ponsero", + "Bartelme", + "Almeida", + "Bigelow", + "Tuteja", + "Ellingson", + "Swetnam", + "Merchant", + "Oxnam", + "Lyons" ], - "joinedAuthorList": "Steven R. Brandt, Bita Hasheminezhad, Nanmiao Wu, Sayef Azad Sakin, Alex R. Bigelow, Katherine E. Isaacs, Kevin Huck, and Hartmut Kaiser" + "joinedAuthorList": "Alise Ponsero, Ryan Bartelme, Gustavo de Oliveira Almeida, Alex Bigelow, Reetu Tuteja, Holly Ellingson, Tyson Swetnam, Nirav Merchant, Maliaca Oxnam, and Eric Lyons", + "shortAuthorList": "Ponsero, Bartelme, Almeida, Bigelow, Tuteja, Ellingson, Swetnam, Merchant, Oxnam, and Lyons" }, "filename": "citation.bib", - "lastmod": "2020-10-16" + "lastmod": "2020-10-24" } }, - "2012_comprehengsive": { - "publication.pdf": { - "url": "/cv/publications/abstracts/2012_comprehengsive/publication.pdf", + "2019_vast_origraph": { + "supplement.pdf": { + "url": "/cv/publications/papers/2019_vast_origraph/supplement.pdf", "path": [ "publications", - "abstracts", - "2012_comprehengsive" + "papers", + "2019_vast_origraph" ], - "name": "publication", + "name": "supplement", "extension": "pdf", - "filename": "publication.pdf", + "filename": "supplement.pdf", + "lastmod": "2020-09-27" + }, + "demo.url": { + "url": "/cv/publications/papers/2019_vast_origraph/demo.url", + "path": [ + "publications", + "papers", + "2019_vast_origraph" + ], + "name": "demo", + "extension": "url", + "contents": "https://youtu.be/bSFf2iD4TLI\n", + "filename": "demo.url", + "lastmod": "2020-12-04" + }, + "abstract.txt": { + "url": "/cv/publications/papers/2019_vast_origraph/abstract.txt", + "path": [ + "publications", + "papers", + "2019_vast_origraph" + ], + "name": "abstract", + "extension": "txt", + "contents": "Networks are a natural way of thinking about many datasets. The data on which a network is based, however, is rarely collected in a form that suits the analysis process, making it necessary to create and reshape networks. Data wrangling is widely acknowledged to be a critical part of the data analysis pipeline, yet interactive network wrangling has received little attention in the visualization research community. In this paper, we discuss a set of operations that are important for wrangling network datasets and introduce a visual data wrangling tool, Origraph, that enables analysts to apply these operations to their datasets. Key operations include creating a network from source data such as tables, reshaping a network by introducing new node or edge classes, filtering nodes or edges, and deriving new node or edge attributes. Our tool, Origraph, enables analysts to execute these operations with little to no programming, and to immediately visualize the results. Origraph provides views to investigate the network model, a sample of the network, and node and edge attributes. In addition, we introduce interfaces designed to aid analysts in specifying arguments for sensible network wrangling operations. We demonstrate the usefulness of Origraph in two Use Cases: first, we investigate gender bias in the film industry, and then the influence of money on the political support for the war in Yemen.\n", + "filename": "abstract.txt", "lastmod": "2020-09-27" }, "citation.bib": { - "url": "/cv/publications/abstracts/2012_comprehengsive/citation.bib", + "url": "/cv/publications/papers/2019_vast_origraph/citation.bib", "path": [ "publications", - "abstracts", - "2012_comprehengsive" + "papers", + "2019_vast_origraph" ], "name": "citation", - "extension": "bib", - "contents": { - "title": "compreheNGSive: A Tool for Exploring Next-Gen Sequencing Variants", - "author": "Bigelow, Alex and Meyer, Miriah and Camp, Nicola J.", - "year": "2012", - "booktitle": "Proceedings of the IEEE Symposium on Biological Data Visualization (BioVis'12)", + "extension": "bib", + "contents": { + "title": "Origraph: Interactive Network Wrangling", + "author": "Bigelow, Alex and Nobre, Carolina and Meyer, Miriah and Lex, Alexander", + "booktitle": "2019 IEEE Conference on Visual Analytics Science and Technology (VAST)", + "pages": "81--92", + "year": "2019", + "organization": "IEEE", + "doi": "10.1109/VAST47406.2019.8986909", "authorList": [ "Alex Bigelow", + "Carolina Nobre", "Miriah Meyer", - "Nicola J. Camp" + "Alexander Lex" ], - "joinedAuthorList": "Alex Bigelow, Miriah Meyer, and Nicola J. Camp" + "authorLastNames": [ + "Bigelow", + "Nobre", + "Meyer", + "Lex" + ], + "joinedAuthorList": "Alex Bigelow, Carolina Nobre, Miriah Meyer, and Alexander Lex", + "shortAuthorList": "Bigelow, Nobre, Meyer, and Lex" }, "filename": "citation.bib", - "lastmod": "2020-09-27" + "lastmod": "2020-10-05" }, - "award.txt": { - "url": "/cv/publications/abstracts/2012_comprehengsive/award.txt", + "description.html": { + "url": "/cv/publications/papers/2019_vast_origraph/description.html", "path": [ "publications", - "abstracts", - "2012_comprehengsive" + "papers", + "2019_vast_origraph" ], - "name": "award", - "extension": "txt", - "contents": "Poster selected for oral presentation\n", - "filename": "award.txt", + "name": "description", + "extension": "html", + "filename": "description.html", "lastmod": "2020-09-27" }, - "meta.json": { - "url": "/cv/publications/abstracts/2012_comprehengsive/meta.json", + "talk.url": { + "url": "/cv/publications/papers/2019_vast_origraph/talk.url", "path": [ "publications", - "abstracts", - "2012_comprehengsive" + "papers", + "2019_vast_origraph" + ], + "name": "talk", + "extension": "url", + "contents": "https://vimeo.com/372531346\n", + "filename": "talk.url", + "lastmod": "2020-10-23" + }, + "publication.pdf": { + "url": "/cv/publications/papers/2019_vast_origraph/publication.pdf", + "path": [ + "publications", + "papers", + "2019_vast_origraph" + ], + "name": "publication", + "extension": "pdf", + "filename": "publication.pdf", + "lastmod": "2020-09-27" + } + } + } + }, + "experience": { + "ta_2.md": { + "url": "/cv/experience/ta_2.md", + "path": [ + "experience" + ], + "name": "ta_2", + "extension": "md", + "contents": { + "content": "", + "data": { + "title": "Teaching Assistant", + "season": "Fall", + "year": 2015, + "meta": [ + "CS 5630 / 6630 Visualization", + "University of Utah, Salt Lake City, UT" + ], + "reference": "with Dr. Alexander Lex, using D3.js", + "links": { + "Course page": "http://dataviscourse.net/2015/" + }, + "referenceList": [ + "Alexander Lex" + ] + }, + "isEmpty": false, + "excerpt": "" + }, + "filename": "ta_2.md", + "lastmod": "2022-08-27" + }, + "genepi.md": { + "url": "/cv/experience/genepi.md", + "path": [ + "experience" + ], + "name": "genepi", + "extension": "md", + "contents": { + "content": "

For two years, I developed and experimented with Next-Generation Sequencing processing and analysis tools. We also worked with large pedigrees from the Utah Population Database.

\n

I gained firsthand exposure to large, messy, and heavily nuanced data. We also grappled with task ambiguity—as these were new, rich resources, they presented truly wicked problems: once we could see one pattern in the data, it made us ask questions that needed an entirely different perspective. I was also able to observe the difficulties, potential errors, and lack of standards and support that domain scientists face when trying to work with new kinds of data.

", + "data": { + "title": "Research Assistant", + "start": 2010, + "stop": 2012, + "meta": [ + "Internal Medicine", + "Division of Genetic Epidemiology", + "University of Utah, Salt Lake City, UT" + ], + "reference": "Advisor: Dr. Nicola J. Camp", + "links": { + "BS Thesis": "/cv#2012_bs_thesis", + "Cancer Research Papers": [ + "/cv#2016_haplotype", + "/cv#2014_targeted" + ] + }, + "referenceList": [ + "Nicola J. Camp" + ] + }, + "isEmpty": false, + "excerpt": "" + }, + "filename": "genepi.md", + "lastmod": "2022-08-27" + }, + "stardog.md": { + "url": "/cv/experience/stardog.md", + "path": [ + "experience" + ], + "name": "stardog", + "extension": "md", + "contents": { + "content": "

At Stardog, I helped design, implement ship, and maintain several user-facing applications (and associated libraries and Cloud UI), used by all of Stardog's customers and beyond. These included:

\n
    \n
  • Stardog Designer, a graph modeling and mapping tool which was largely based off my Origraph research work
    • \n
  • Stardog Explorer, a simple node-link diagram visualization tool with an accessible (yet very expressive) visual query building interface
    • \n
  • Stardog Studio, an IDE for writing and editing queries, and managing Stardog databases and virtual graphs
    • \n
\n

I was also heavily involved in the design and integration of Stardog Voicebox—a Large Language Model-powered chat assistant that translated natural language into SPARQL queries, executed the queries against data in Stardog, and summarized the results with an explainable UX with citations and a visual rendering of the query, that communicated exactly how the AI was able to find its answers.

", + "data": { + "title": "Software Engineer", + "start": 2021, + "stop": 2024, + "meta": [ + "Stardog Union", + "Arlington, VA" + ], + "reference": "Mentors: Annee Barrett, Dr. Jason Rogers, Laura Firey Monroe, Dr. Michael Grove, Paul Ambro", + "referenceList": [ + "Barrett", + "Jason Rogers", + "Laura Firey Monroe", + "Michael Grove", + "Paul Ambro" + ] + }, + "isEmpty": false, + "excerpt": "" + }, + "filename": "stardog.md", + "lastmod": "2022-08-27" + }, + "kitware.md": { + "url": "/cv/experience/kitware.md", + "path": [ + "experience" + ], + "name": "kitware", + "extension": "md", + "contents": { + "content": "

During this seven-month internship, I was privileged to work on Resonant Lab, a system that enables connecting arbitrary datasets to arbitrary visualizations. This work culminated in a Best Paper Award at the Visualization In Practice Workshop (VIP '16).

\n

I gained a lot of experience with real-world software development, and building better-quality software than I normally have time for in academia was incredibly satisfying. Working in an industry research lab like this was great because it gave me the flexibility to think deeply about problems and approach them in non-conventional ways, but at the same time, it provided the support and priority structure to develop high-quality software. Working for Kitware was also a valuable experience because of its focus on open-source development.

", + "data": { + "title": "Research Intern", + "season": "Spring, Summer", + "year": 2016, + "meta": [ + "Kitware, Inc.", + "Clifton Park, NY" + ], + "reference": "Mentors: Dr. Jeff Baumes, Dr. Roni Choudhury", + "links": { + "VIP Best Paper": "/cv#2016_vip_resonant_lab", + "Resonant Lab": "/projects#resonant_lab" + }, + "referenceList": [ + "Jeff Baumes", + "Roni Choudhury" + ] + }, + "isEmpty": false, + "excerpt": "" + }, + "filename": "kitware.md", + "lastmod": "2020-12-04" + }, + "sci.md": { + "url": "/cv/experience/sci.md", + "path": [ + "experience" + ], + "name": "sci", + "extension": "md", + "contents": { + "content": "

As a PhD student, I researched the effects that data can have on graphic designers as they create visualizations, how to support more iterative workflows between programming and drawing, and how to better support ideation about different network data abstractions.

", + "data": { + "title": "Research Assistant", + "start": 2013, + "stop": 2018, + "meta": [ + "School of Computing", + "Scientific Computing and Imaging (SCI) Institute", + "University of Utah, Salt Lake City, UT" + ], + "reference": "Advisor: Dr. Miriah Meyer", + "referenceList": [ + "Miriah Meyer" + ] + }, + "isEmpty": false, + "excerpt": "" + }, + "filename": "sci.md", + "lastmod": "2020-12-04" + }, + "ua.md": { + "url": "/cv/experience/ua.md", + "path": [ + "experience" + ], + "name": "ua", + "extension": "md", + "contents": { + "content": "

As a postdoc, I researched, published, and submitted a grant (that wasn't funded) to study the impacts that different data abstractions can have on visualization design and analysis. I also helped advise two PhD students conducting design studies and building visualization systems for High Performance Computing researchers.

", + "data": { + "title": "Postdoctoral Researcher", + "start": 2019, + "stop": 2021, + "meta": [ + "Department of Computer Science", + "University of Arizona, Tucson, AZ" + ], + "reference": "Advisor: Dr. Katherine E Isaacs", + "referenceList": [ + "Katherine E Isaacs" + ] + }, + "isEmpty": false, + "excerpt": "" + }, + "filename": "ua.md", + "lastmod": "2022-08-27" + }, + "ta_1.md": { + "url": "/cv/experience/ta_1.md", + "path": [ + "experience" + ], + "name": "ta_1", + "extension": "md", + "contents": { + "content": "", + "data": { + "title": "Teaching Assistant", + "season": "Fall", + "year": 2014, + "meta": [ + "CS 5630 / 6630 Visualization", + "University of Utah, Salt Lake City, UT" ], - "name": "meta", - "extension": "json", - "contents": { - "award": "Poster Selected for Oral Presentation" + "reference": "with Dr. Miriah Meyer, using Processing", + "links": { + "Course page": "https://www.cs.utah.edu/~miriah/teaching/cs6630/" }, - "filename": "meta.json", - "lastmod": "2020-09-27" - } + "referenceList": [ + "Miriah Meyer" + ] + }, + "isEmpty": false, + "excerpt": "" }, - "2017_fellow_tool_builders": { - "poster.pdf": { - "url": "/cv/publications/abstracts/2017_fellow_tool_builders/poster.pdf", - "path": [ - "publications", - "abstracts", - "2017_fellow_tool_builders" + "filename": "ta_1.md", + "lastmod": "2020-12-04" + }, + "brusci.md": { + "url": "/cv/experience/brusci.md", + "path": [ + "experience" + ], + "name": "brusci", + "extension": "md", + "contents": { + "content": "

I volunteered on the SCI Institute's student committee. Responsibilities have included:

\n
    \n
  • Deep involvement in planning and carrying out the SCI X exhibition in 2016. This included creating an interactive map for a display table and visitors' devices
    • \n
  • Planning and carrying out Institute parties. This included mocking up an interface for managing an in-house ping pong tournament
    • \n
", + "data": { + "title": "Committee Member", + "start": 2015, + "stop": 2018, + "service": true, + "meta": [ + "Scientific Computing and Imaging Institute", + "Student Activity Committee", + "University of Utah, Salt Lake City, UT" ], - "name": "poster", - "extension": "pdf", - "filename": "poster.pdf", - "lastmod": "2020-09-27" + "hideInPrint": true, + "reference": "Advisor: Dr. Greg Jones", + "links": { + "SCI X Map": "/projects#scix_map", + "Ping Pong Tournament": "/projects#ping_pong_tournament", + "InfoVis Poster": "/cv#2017_fellow_tool_builders" + }, + "referenceList": [ + "Greg Jones" + ] }, - "abstract.txt": { - "url": "/cv/publications/abstracts/2017_fellow_tool_builders/abstract.txt", - "path": [ - "publications", - "abstracts", - "2017_fellow_tool_builders" - ], - "name": "abstract", - "extension": "txt", - "contents": "While it is true that fellow tool builders can threaten the success of a design study, there are also advantages to working with individuals that have strong software development skills. We present a review of two information visualization projects using thematic analysis, that provides additional insight and guidance for collaborating with people that have strong software development skills. Additionally, we discuss minor implications for the design of node-link diagrams and adjacency matrices, and report observed differences in engagement with respect to touch tables versus traditional keyboard, mouse, and monitor configurations.\n", - "filename": "abstract.txt", - "lastmod": "2020-09-27" + "isEmpty": false, + "excerpt": "" + }, + "filename": "brusci.md", + "lastmod": "2021-09-30" + }, + "resbaz.md": { + "url": "/cv/experience/resbaz.md", + "path": [ + "experience" + ], + "name": "resbaz", + "extension": "md", + "contents": { + "content": "

I benefitted from, and endeavored to assist with, a University of Arizona campus outreach group that provided regular meetups for people on campus and members of the community to help each other with applied programming or data challenges.

\n

We also organized a free weeklong series of workshops that provided training in a variety of data science topics.

", + "data": { + "title": "Steering Committee Member", + "start": 2019, + "stop": "Present", + "service": true, + "meta": [ + "Arizona Research Bazaar Steering Committee", + "University of Arizona, Tucson, AZ" + ] }, - "publication.pdf": { - "url": "/cv/publications/abstracts/2017_fellow_tool_builders/publication.pdf", - "path": [ - "publications", - "abstracts", - "2017_fellow_tool_builders" - ], - "name": "publication", - "extension": "pdf", - "filename": "publication.pdf", - "lastmod": "2020-09-27" + "isEmpty": false, + "excerpt": "" + }, + "filename": "resbaz.md", + "lastmod": "2020-12-03" + }, + "reviewing.md": { + "url": "/cv/experience/reviewing.md", + "path": [ + "experience" + ], + "name": "reviewing", + "extension": "md", + "contents": { + "content": "", + "data": { + "title": "Peer Reviewer", + "start": 2015, + "stop": 2024, + "service": true, + "meta": [ + "IEEE VIS Conference, IEEE Transactions on Visualization and Computer Graphics (2016–2023), Short Papers Program Committee (2020)", + "Eurovis VGTC Conference on Visualization (2016, 2020–2022)", + "ACM CHI Conference on Human Factors in Computing Systems (2015, 2017–2022, 2024)", + "Workshop on Visualization in Practice (2017)", + "alt.VIS Workshop (2021)" + ] }, - "supplement.md": { - "url": "/cv/publications/abstracts/2017_fellow_tool_builders/supplement.md", - "path": [ - "publications", - "abstracts", - "2017_fellow_tool_builders" + "isEmpty": false, + "excerpt": "" + }, + "filename": "reviewing.md", + "lastmod": "2021-09-30" + }, + "dsf.md": { + "url": "/cv/experience/dsf.md", + "path": [ + "experience" + ], + "name": "dsf", + "extension": "md", + "contents": { + "content": "

The University of Arizona Data Science Fellow program included a period of intense training in which each fellow instructed the others in specific data science disciplines; for example, in my case, I developed and conducted a series of trainings in data visualization.

\n

We also engaged with University projects in the Health Sciences and adjacent organizations; my involvement included working with Arizona Research Bazaar to help with campus computing outreach efforts, as well as HCW HOSTED to provide resources for healthcare workers during the COVID-19 pandemic.

", + "data": { + "title": "Data Science Fellow", + "start": 2020, + "stop": 2020, + "meta": [ + "Health Sciences", + "University of Arizona, Tucson, AZ" ], - "name": "supplement", - "extension": "md", - "contents": { - "content": "

This file summarizes the raw observations, open codes, and resulting themes.

\n

Collaborators

\n

| ID | Role | Gender | Research Area |\n|--------|---------------------|--------|---------------------------|\n| I1 | Mid Grad Student | F | Biomedical Computation |\n| I2 | Mid Grad Student | F | Biomedical Computation |\n| I3 | Staff Developer | F | Scientific Computing |\n| I4 | Research Faculty | M | Information Visualization |\n| I5 | Senior Grad Student | M | Biomedical Computation |\n| I6 | Senior Grad Student | M | Biomedical Computation |\n| I7 | Senior Grad Student | M | Biomedical Computation |\n| I8 | New Grad Student | F | Scientific Visualization |

\n

Raw observations

\n

The very raw data used for this poster takes the form of git commit messages, git histories, emails, Slack conversations, and group meeting notes.\nRather than include all of that data directly (that would include identifying information, etc), extracts of the raw events surrounding the development of each system are summarized below.

\n

Open House Map Extracts

\n
    \n
  • M1: We used text CSV files on GitHub to hold all the information about what groups would be where, and, later, what individual posters or presentations would be in what area. These csv files had to be refactored a number of times
    • \n
  • M2: Though the student committee worked hard for weeks to get details, I ended up having to come in at night to collect poster location information myself, once the posters were finally set up. I3's assigned area was particularly problematic, because the location was changed last-minute
    • \n
  • M3: Using an Illustrator SVG map made annotating (e.g. adding restrooms to the map) / changing area shapes easy; most changes in the git history were changes to the spaceAssignments.csv file
    • \n
  • M4: I4 provided useful feedback about the width of the selection bars above each poster name (they were initially squares and hard to click directly, even though the whole text block was technically clickable), but also provided (too much?) feedback about things like typography
    • \n
  • M5: An institution-wide meeting (mostly about making sure people created / printed their posters on time) quickly devolved into a debate about the interface… particularly with respect to the map orientation (should North be up? But people exit the elevator, and initially encounter the interactive interface facing South…). However, an important development in this meeting occurred when the task abstraction of the interface changed---some participants indicated that they knew specific visitors that would want to be able to locate individual posters.
    • \n
  • M6: Public display on a touch table likely contributed to high engagement - my personal demo was on an equally-sized monitor immediately off the elevator, but most visitors would walk right past me to the touch display in the room behind me (of course, I didn't actively try to stop people to see my demo, and it makes sense that people would want to first orient themselves in a new environment)
    • \n
\n

Ping Pong Tournament Extracts

\n
    \n
  • P1: Instead of CSV files on GitHub, we used Google forms / sheets as a pseudo-database for the ping pong tournament. We still used GitHub for hosting the site, but this meant that committee members could check / edit the spreadsheets easily
    • \n
  • P2: Setting up a debug / simulation mode was helpful during the live ping pong deployment - I6 in particular responded quickly to requests to beta test changes to the site before they went live. Because of the google spreadsheets setup, it was easy to see and debug what tests he used to try (and, in some cases, succeed) to trigger bugs.
    • \n
  • P3: I5, I6, and I7 had very specific ideas of how the pool play / bracket should work. As such, I planned (and succeeded) to outsource the seeding of the bracket to them via a Google spreadsheet
    • \n
  • P4: Shortly after the first debugging deployment, I8 designed and printed promotional posters using the background image… but chose a very different font style and color scheme. Rather than reprint the posters, we felt it best to refactor the interactive system.
    • \n
  • P5: This interface required typing in information---initially, we planned to deploy the interface on a touch table, as we had with the open house map. The touch table has a built-in keyboard that can be swiped in from the side---but we needed to add an icon to the interface to make this clear. However, due to a more important project needing the touch table, we had to instead deploy the interface on a monitor by the elevator (actually the same monitor where I gave my demo in the open house), with a keyboard and mouse attached
    • \n
  • P6: We initially anticipated more participants---because the limited number that actually signed up was much lower (the vis deadline was partly to blame---we later heard that many more would have signed up, but they were too busy with submissions), we decided to include everyone in the bracket. This necessitated a last-minute rewrite of the code to include BYE / PASS nodes for the highest-seeded players
    • \n
  • P7: It proved difficult to get people to actually play their games, particularly when the scheduled players didn't know each other well. Eventually, we had to add forfeits to the pool play phase (again, necessitating a last-minute redesign of the system). This happened again in the bracket---some students began leaving for the summer. Luckily, the few that had left were able to nominate the player they had most recently defeated to play for them, and the change was a simple adjustment to the spreadsheets (more drastic rewrites of the system were not necessary)
    • \n
  • P8: Our initial plan was for all participants to pick a charity to represent (I1 provided a CSV list of 503(c)(3) charities), and non-players could still participate by \"betting\" on players. However, this garnered little attention / participation. Toward the beginning of the bracket phase, I6 suggested that we implement a March Madness-style approach, where people could submit their own brackets, and award a secondary prize to the charity picked by the most accurate bracket. Unfortunately, this was too difficult to implement in the short amount of time left in the tournament.
    • \n
  • P9: Having the public display also appeared to result in high engagement, though not as much as I observed with the touch table. Passers-by seemed to be hesitant to use the keyboard / mouse… this may have had something to do with the permanent nature of the display (attached to the wall) - normally, the monitor showed a looping video of demonstrations, that people would not normally interfere with.
    • \n
  • P10: Some passers-by reported confusion about the triangular edges, particularly in the node-link diagram (are triangles arrowheads pointing to the winner, or does the larger side indicate the winner)?
    • \n
  • P11: Though most people that interacted with the interface were very technically savvy, the pool play adjacency matrices proved confusing to some people (not all, however… some people even commented on how intuitive they were). In their design, I3 provided very useful feedback---initially, I displayed an arrow for an already-played game, pointing to the winner. However, I3 made it clear that this was confusing; instead, redundantly displaying the name of the winner in the cell made more sense.
    • \n
  • P12: I6 contributed a very minor code fix
    • \n
\n

Open Codes

\n
    \n
  • O1: Last-minute system adjustments were common (M2, P4, P5, P6, P7, P8)
    • \n
  • O2: Clever engineering tricks made most last-minute adjustments easier to handle (M3, P1, P2, P7)
    • \n
  • O3: Actual code contributions from collaborators were rare (P12)
    • \n
  • O4: Spreadsheets encouraged more collaborator help (M1, P1)
    • \n
  • O5: Overall, mixed results getting data from collaborators (M2, P2, P3, P8)
    • \n
  • O6: Confusion about triangular edges (P10)
    • \n
  • O7: Confusion / intuition about rotated adjacency matrices (P11)
    • \n
  • O8: Collaborators' feedback (mostly) insightful (M4, M5, P2, P11)
    • \n
  • O9: Touch table more engaging than monitor + keyboard / mouse (M6, P9)
    • \n
\n

Themes

\n

Collaborator Participation

\n
    \n
  • A1: Collaborator technical involvement in the project varied; personality seemed to dictate whether and how much people contributed, rather than interest in the overall project or interest in the technical aspects (O3, O4, O5). Technical involvement did not seem to have any relationship with relevant technical skills (O3; I6 is not a web developer).
    • \n
  • A2: Collaborators most readily participated when the tools were familiar; google sheets (even with strict rules about structure) were the most freely adjusted. Github CSV files came in second, beta testing the interface itself came in third, and the interface code was barely touched (O3, O4, O5).
    • \n
\n

Collaborator Feedback

\n
    \n
  • A3: Most feedback was helpful; compared to non-developer users in typical design studies, people seemed more willing to provide critique (O8). The kinds of critique that collaborators suggested tended to be more bounded by their technical knowledge of what is easily changed, and what is difficult to implement (01, 02, 08)
    • \n
  • A4: Some feedback was too specific or failed to capture the scope of the project; dealing with this gracefully is tricky. However, it was a pitfall to automatically assume that all feedback was too specific (O8)
    • \n
\n

Implications for Visualization Techniques and Deployment

\n
    \n
  • A5: Adjacency matrices were confusing to a subset of a technical audience (O7)! Artifact of rotated design?
    • \n
  • A6: Triangles as arrows are ambiguous (O6)
    • \n
  • A7: Touch table more engaging than fixed monitor (O9)
    • \n
\n

Key Takeaways

\n
    \n
  • Just because a collaborator has the technical ability and the time to contribute, that doesn't mean that they will (A1, A2)
    • \n
  • The opposite is also true: just because a collaborator doesn't appear to have the technical ability or the time to contribute, that doesn't mean that they won't (A1, A2)
    • \n
  • Concern about working with fellow tool builders is warranted, but they should not necessarily be avoided---their expertise can be an incredible asset (A3, A4)
    • \n
  • Some minor details of node-link diagrams and adjacency matrices can have a profound effect on the ability of users to make sense of what is represented (A5, A6)---where these are employed, a legend is probably necessary
    • \n
  • Touch table vs traditional display: the former seems to naturally produce more engagement / willingness to mess with the system (A7)
    • \n
", - "data": {}, - "isEmpty": false, - "excerpt": "" + "reference": "Mentors: Dr. Alex Thome, Dr. Maliaca Oxnam, Dr. Eric Lyons", + "links": { + "PLOS Comp. Bio. Paper": "/cv#2020_ten_rules", + "HCW HOSTED Project": "/projects#hcw_hosted", + "Arizona Research Bazaar": "/cv#resbaz" }, - "filename": "supplement.md", - "lastmod": "2020-09-27" - }, - "video.mp4": { - "url": "/cv/publications/abstracts/2017_fellow_tool_builders/video.mp4", - "path": [ - "publications", - "abstracts", - "2017_fellow_tool_builders" - ], - "name": "video", - "extension": "mp4", - "filename": "video.mp4", - "lastmod": "2020-09-27" + "referenceList": [ + "Alex Thome", + "Maliaca Oxnam", + "Eric Lyons" + ] }, - "citation.bib": { - "url": "/cv/publications/abstracts/2017_fellow_tool_builders/citation.bib", - "path": [ - "publications", - "abstracts", - "2017_fellow_tool_builders" + "isEmpty": false, + "excerpt": "" + }, + "filename": "dsf.md", + "lastmod": "2020-12-04" + }, + "ibm.md": { + "url": "/cv/experience/ibm.md", + "path": [ + "experience" + ], + "name": "ibm", + "extension": "md", + "contents": { + "content": "

During this three-month internship, we developed Jacob's Ladder, a system that supports traversing a large graph database in aggregate using graph pivots.

\n

Apache TinkerPop3 was released midway through this project, just as we had switched from a Neo4j graph database to a Titan database. I learned a lot about graph databases and graph query languages, and learned hard but valuable lessons about good documentation, developing for a moving target, and the dangers of vendor lock-in.

", + "data": { + "title": "Research Intern", + "season": "Summer", + "year": 2015, + "meta": [ + "IBM Research", + "Cambridge, MA" ], - "name": "citation", - "extension": "bib", - "contents": { - "title": "Reflections on Working With Fellow Tool Builders", - "author": "Bigelow, Alex", - "year": "2017", - "booktitle": "Proceedings of the IEEE Information Visualization Conference-Posters (InfoVis'17)", - "authorList": [ - "Alex Bigelow" - ], - "joinedAuthorList": "Alex Bigelow" + "reference": "Mentor: Dr. Megan Monroe", + "links": { + "PacificVis Paper": "/cv#jacobs_ladder", + "Project": "/projects#jacobs_ladder" }, - "filename": "citation.bib", - "lastmod": "2020-09-27" + "referenceList": [ + "Megan Monroe" + ] }, - "fastForward.mp4": { - "url": "/cv/publications/abstracts/2017_fellow_tool_builders/fastForward.mp4", - "path": [ - "publications", - "abstracts", - "2017_fellow_tool_builders" - ], - "name": "fastForward", - "extension": "mp4", - "filename": "fastForward.mp4", - "lastmod": "2020-09-27" - } - } + "isEmpty": false, + "excerpt": "" + }, + "filename": "ibm.md", + "lastmod": "2020-12-04" } } } \ No newline at end of file diff --git a/views/CvView/mapping.sms b/views/CvView/mapping.sms index 539fe09..6491270 100644 --- a/views/CvView/mapping.sms +++ b/views/CvView/mapping.sms @@ -20,12 +20,20 @@ FROM JSON { }, "publications": { "?publicationType": { - "?publicationId": { + "?citationKey": { + "abstract.txt": { + "contents": "?abstractContent", + }, "citation.bib": { "contents": { "title": "?publicationTitle", - "authorList": [ "?coauthorPerson" ] + "authorList": [ "?coauthor" ] } + }, + "?resourceId" : { + "url": "?resourceUrl", + "name": "?resourceName", + "lastmod": "?lastmod" } } } @@ -41,7 +49,7 @@ TO { ?coaPerson a foaf:Person ; rdfs:label ?coaPersonLabel ; :collaborated_on ?pub ; - :name ?coauthorPerson . + :name ?coauthor . ?pub a :Publication ; rdfs:label ?pubTitle ; @@ -49,18 +57,30 @@ TO { ?exp a :Work_Experience ; rdfs:label ?expTitle . + + ?res a :Publication_Resource ; + rdfs:label ?resLabel ; + :url ?resUrl ; + :last_modified ?lastModified ; + :name ?resName . } WHERE { BIND(TEMPLATE("tag:alex:bigelow:cv:graph:Person_{referencePerson}") AS ?refPerson) BIND(xsd:string(?referencePerson) AS ?refPersonLabel) - BIND(TEMPLATE("tag:alex:bigelow:cv:graph:Person_{coauthorPerson}") AS ?coaPerson) - BIND(xsd:string(?coauthorPerson) AS ?coaPersonLabel) + BIND(TEMPLATE("tag:alex:bigelow:cv:graph:Person_{coauthor}") AS ?coaPerson) + BIND(xsd:string(?coauthor) AS ?coaPersonLabel) - BIND(TEMPLATE("tag:alex:bigelow:cv:graph:Publication_{publicationId}") AS ?pub) + BIND(TEMPLATE("tag:alex:bigelow:cv:graph:Publication_{citationKey}") AS ?pub) BIND(xsd:string(?publicationTitle) AS ?pubTitle) BIND(xsd:string(?publicationType) AS ?pubType) BIND(TEMPLATE("tag:alex:bigelow:cv:graph:Publication_{experienceId}") AS ?exp) BIND(xsd:string(?experienceTitle) AS ?expTitle) + + BIND(TEMPLATE("tag:alex:bigelow:cv:graph:Publication_Resource_{citationKey}_{resourceId}") AS ?res) + BIND(xsd:string(?resourceId) AS ?resLabel) + BIND(xsd:string(?resourceUrl) AS ?resUrl) + BIND(xsd:string(?resourceName) AS ?resName) + BIND(xsd:date(?lastmod) AS ?lastModified) } diff --git a/views/CvView/model.ttl b/views/CvView/model.ttl index 11a972d..ca082f9 100644 --- a/views/CvView/model.ttl +++ b/views/CvView/model.ttl @@ -61,5 +61,13 @@ foaf:Person a owl:Class ; rdfs:range xsd:string . :name a owl:DatatypeProperty ; rdfs:label "name" ; - rdfs:domain foaf:Person ; + rdfs:domain foaf:Person, :Publication_Resource ; + rdfs:range xsd:string . +:url a owl:DatatypeProperty ; + rdfs:label "url" ; + rdfs:domain :Publication_Resource ; rdfs:range xsd:string . +:last_modified a owl:DatatypeProperty ; + rdfs:label "last modified" ; + rdfs:domain :Publication_Resource ; + rdfs:range xsd:date . \ No newline at end of file diff --git a/views/CvView/style.less b/views/CvView/style.less index 265c444..13575eb 100644 --- a/views/CvView/style.less +++ b/views/CvView/style.less @@ -1,39 +1,39 @@ /* eb-garamond-regular - latin */ @font-face { - font-family: "EB Garamond"; + font-family: 'EB Garamond'; font-style: normal; font-weight: 400; - src: url("fonts/eb-garamond-v12-latin-regular.eot"); /* IE9 Compat Modes */ - src: local(""), - url("fonts/eb-garamond-v12-latin-regular.eot?#iefix") - format("embedded-opentype"), - /* IE6-IE8 */ url("fonts/eb-garamond-v12-latin-regular.woff2") - format("woff2"), - /* Super Modern Browsers */ url("fonts/eb-garamond-v12-latin-regular.woff") - format("woff"), - /* Modern Browsers */ url("fonts/eb-garamond-v12-latin-regular.ttf") - format("truetype"), + src: url('fonts/eb-garamond-v12-latin-regular.eot'); /* IE9 Compat Modes */ + src: local(''), + url('fonts/eb-garamond-v12-latin-regular.eot?#iefix') + format('embedded-opentype'), + /* IE6-IE8 */ url('fonts/eb-garamond-v12-latin-regular.woff2') + format('woff2'), + /* Super Modern Browsers */ url('fonts/eb-garamond-v12-latin-regular.woff') + format('woff'), + /* Modern Browsers */ url('fonts/eb-garamond-v12-latin-regular.ttf') + format('truetype'), /* Safari, Android, iOS */ - url("fonts/eb-garamond-v12-latin-regular.svg#EBGaramond") format("svg"); /* Legacy iOS */ + url('fonts/eb-garamond-v12-latin-regular.svg#EBGaramond') format('svg'); /* Legacy iOS */ } /* eb-garamond-smallCaps - latin */ @font-face { - font-family: "EB Garamond SC"; + font-family: 'EB Garamond SC'; font-style: normal; font-weight: 400; - src: url("fonts/eb-garamond-sc-v12-latin-regular.eot"); /* IE9 Compat Modes */ - src: local(""), - url("fonts/eb-garamond-sc-v12-latin-regular.eot?#iefix") - format("embedded-opentype"), - /* IE6-IE8 */ url("fonts/eb-garamond-sc-v12-latin-regular.woff2") - format("woff2"), + src: url('fonts/eb-garamond-sc-v12-latin-regular.eot'); /* IE9 Compat Modes */ + src: local(''), + url('fonts/eb-garamond-sc-v12-latin-regular.eot?#iefix') + format('embedded-opentype'), + /* IE6-IE8 */ url('fonts/eb-garamond-sc-v12-latin-regular.woff2') + format('woff2'), /* Super Modern Browsers */ - url("fonts/eb-garamond-sc-v12-latin-regular.woff") format("woff"), - /* Modern Browsers */ url("fonts/eb-garamond-sc-v12-latin-regular.ttf") - format("truetype"), + url('fonts/eb-garamond-sc-v12-latin-regular.woff') format('woff'), + /* Modern Browsers */ url('fonts/eb-garamond-sc-v12-latin-regular.ttf') + format('truetype'), /* Safari, Android, iOS */ - url("fonts/eb-garamond-sc-v12-latin-regular.svg#EBGaramond") format("svg"); /* Legacy iOS */ + url('fonts/eb-garamond-sc-v12-latin-regular.svg#EBGaramond') format('svg'); /* Legacy iOS */ } .CV { @@ -58,7 +58,8 @@ } h5 { background-color: var(--background-color-softer); - padding: 0.25em; + padding: 1em 1em 0.65em 1em; + text-align: center; font-weight: var(--heavy-font-weight); } h2 + div h5 { @@ -74,7 +75,7 @@ color: var(--accent-color); margin-bottom: 0; &:before { - content: "\2606"; + content: '\2606'; position: absolute; left: -1em; bottom: 0px; @@ -126,10 +127,10 @@ .printHelper { visibility: hidden; h1 { - font-family: "EB Garamond SC", serif; + font-family: 'EB Garamond SC', serif; } p { - font-family: "EB Garamond", serif; + font-family: 'EB Garamond', serif; } } @@ -140,24 +141,27 @@ html, body { background: white; - font-family: "EB Garamond", serif; + font-family: 'EB Garamond', serif; color: black !important; font-size: 12pt; overflow: visible; height: auto; margin: 0; padding: 0; - -webkit-print-color-adjust: exact !important; + print-color-adjust: exact !important; /* Note to self: uncomment this when debugging print layout */ width: 8.5in; } + .MenuView, .TooltipView, .hideInPrint { display: none !important; } + .CV { + margin: auto; justify-content: space-between; & > .column { max-width: 24rem; @@ -168,7 +172,7 @@ h4, h5, strong { - font-family: "EB Garamond SC", serif; + font-family: 'EB Garamond SC', serif; page-break-after: avoid; margin-bottom: 0; margin-top: 0; @@ -184,9 +188,8 @@ } } h5 { - letter-spacing: 2pt; - background-color: #ccc; - color: white; + letter-spacing: normal; + background-color: #fff; padding: 0.1em 0.5em; margin-top: 1rem; } @@ -224,6 +227,16 @@ font-size: 0.75em; } + .meta, + .reference, + .joinedAuthorList { + line-height: 1.25em; + } + + .title { + font-size: 9pt; + } + .entry { break-inside: avoid; } diff --git a/views/MenuView/MenuView.js b/views/MenuView/MenuView.js index 841f871..fc067e7 100755 --- a/views/MenuView/MenuView.js +++ b/views/MenuView/MenuView.js @@ -71,9 +71,15 @@ class MenuView extends uki.View { window.location = temp + 'gm' + 'ail.c' + 'om'; }; } - const primary = window.location.pathname === page.url || + const primary = page.forcePrimary; + + /* + Uncomment to go back to primary being the current page + window.location.pathname === page.url || window.location.pathname + '.html' === page.url || (window.location.pathname === '/' && page.url === '/index.html'); + */ + const spec = { label: page.title, img: page.icon, diff --git a/views/MenuView/default.json b/views/MenuView/default.json index 0a19c43..21947c4 100755 --- a/views/MenuView/default.json +++ b/views/MenuView/default.json @@ -6,7 +6,8 @@ }, { "url": "/funding.html", - "title": "Consulting", + "title": "Hire Me!", + "forcePrimary": true, "icon": "/img/fund.svg", "subMenu": [ {