stjude/proteinpaint
Nov 2024 – Jun 2026
20 Months active
Languages Used
JavaScriptTextTypeScriptJSONMarkdownRHTMLPython
Technical Skills
Backend DevelopmentCode OrganizationD3.jsDOM ManipulationData VisualizationDocumentation
Colleen Reilly
PROFILE
Colleen Reilly
Over 20 months, contributed to the stjude/proteinpaint repository by building and refining advanced data visualization and analytics workflows for genomics and single-cell research. Developed interactive charting features, robust plotting infrastructure, and scalable UI components using TypeScript, JavaScript, and D3.js. Focused on maintainable architecture through MVVM patterns, modular component design, and comprehensive test coverage. Enhanced reliability with strict data validation, error handling, and backend integration, while improving user experience with dynamic controls, accessibility, and responsive layouts. Regularly updated documentation and release notes, ensuring clear communication and reproducibility. The work enabled efficient exploratory analysis and supported complex biological data interpretation at scale.
Overall Statistics
Feature vs Bugs
65%Features
Repository Contributions
1,040Total
Bugs
197
Commits
1,040
Features
364
Lines of code
66,094
Activity Months20
Your Network
46 peopleSame Organization
@stjude.org17
PPTeam CIMember
aacicMember
Andrew WillemsMember
Gavriel MattMember
gavrielmMember
Haidong YiMember
Jay KnightMember
WangMember
JamelMember
Shared Repositories
29
aacicMember
Airen Zaldivar PerazaMember
Andrew WillemsMember
congyu-luMember
Edward MalinowskiMember
Gavriel MattMember
gavrielmMember
Jay KnightMember
WangMember
Work History
June 2026
55 Commits • 14 Features
Jun 1, 2026June 2026 monthly summary for stjude/proteinpaint focused on delivering robust data visualization and analysis capabilities, while stabilizing plotting UI, expanding meta-analysis features, and hardening single-cell data routes.
55 Commits • 14 Features
Jun 1, 2026June 2026 monthly summary for stjude/proteinpaint focused on delivering robust data visualization and analysis capabilities, while stabilizing plotting UI, expanding meta-analysis features, and hardening single-cell data routes.
June 2026
May 2026
22 Commits • 4 Features
May 1, 2026May 2026 monthly summary for stjude/proteinpaint focused on delivering robust UI enhancements, stronger data integrity checks, and expanded test coverage to support reliable releases and improved data exploration for researchers. The work emphasized business value through more efficient data visualization, fewer UI regressions, and clearer release documentation.
May 2026
22 Commits • 4 Features
May 1, 2026May 2026 monthly summary for stjude/proteinpaint focused on delivering robust UI enhancements, stronger data integrity checks, and expanded test coverage to support reliable releases and improved data exploration for researchers. The work emphasized business value through more efficient data visualization, fewer UI regressions, and clearer release documentation.
April 2026
112 Commits • 49 Features
Apr 1, 2026April 2026 — stjude/proteinpaint monthly summary: Implemented an enhanced single-cell (SC) plotting workflow with a new Summary plot capability and per-plot SCCT term selection, enabling clearer analyses and report-ready visuals. Strengthened rendering stability and data handling for SC plots, including bounds enforcement for child/subplots and reliable SCCT term initialization. Improved UI/UX with dictionary-launch improvements and tooltip behavior for single-cell plots. Updated tests, documentation, and release notes to reflect code changes and prevent regressions.
112 Commits • 49 Features
Apr 1, 2026April 2026 — stjude/proteinpaint monthly summary: Implemented an enhanced single-cell (SC) plotting workflow with a new Summary plot capability and per-plot SCCT term selection, enabling clearer analyses and report-ready visuals. Strengthened rendering stability and data handling for SC plots, including bounds enforcement for child/subplots and reliable SCCT term initialization. Improved UI/UX with dictionary-launch improvements and tooltip behavior for single-cell plots. Updated tests, documentation, and release notes to reflect code changes and prevent regressions.
April 2026
March 2026
51 Commits • 12 Features
Mar 1, 2026March 2026 monthly summary for stjude/proteinpaint focused on delivering a major architecture refactor, strengthening data validation, and expanding test coverage to boost reliability, maintainability, and speed of delivery. The work emphasized business value through data integrity, easier onboarding for new vocab/TermTypes usage, and more robust CI/QA readiness.
March 2026
51 Commits • 12 Features
Mar 1, 2026March 2026 monthly summary for stjude/proteinpaint focused on delivering a major architecture refactor, strengthening data validation, and expanding test coverage to boost reliability, maintainability, and speed of delivery. The work emphasized business value through data integrity, easier onboarding for new vocab/TermTypes usage, and more robust CI/QA readiness.
February 2026
40 Commits • 20 Features
Feb 1, 2026February 2026 monthly summary for stjude/proteinpaint: Focused on improving CNV visualization fidelity, expanding color-scale driven interactions, and strengthening code quality and test coverage. Delivered key features enabling CNV input from the color scale in the matrix, improved color scale handling with absMax cell fills, correct tick computation, and deduplication defaults. Enhanced UI/UX with standard matrix menu from the SVG legend label and related usability improvements. Fixed critical bugs affecting rendering, filtering, input validation, and tooltips, and advanced TypeScript migration and test infrastructure. These changes deliver clearer, more reliable visualizations, reduce user error, and support scalable color-scale features across datasets.
40 Commits • 20 Features
Feb 1, 2026February 2026 monthly summary for stjude/proteinpaint: Focused on improving CNV visualization fidelity, expanding color-scale driven interactions, and strengthening code quality and test coverage. Delivered key features enabling CNV input from the color scale in the matrix, improved color scale handling with absMax cell fills, correct tick computation, and deduplication defaults. Enhanced UI/UX with standard matrix menu from the SVG legend label and related usability improvements. Fixed critical bugs affecting rendering, filtering, input validation, and tooltips, and advanced TypeScript migration and test infrastructure. These changes deliver clearer, more reliable visualizations, reduce user error, and support scalable color-scale features across datasets.
February 2026
January 2026
38 Commits • 14 Features
Jan 1, 2026January 2026 - ProteinPaint: Delivered core data-visualization and charting improvements, with a strong emphasis on data request reliability, UX clarity, and scalable architecture. Enhanced test coverage and release hygiene to support faster iteration.
January 2026
38 Commits • 14 Features
Jan 1, 2026January 2026 - ProteinPaint: Delivered core data-visualization and charting improvements, with a strong emphasis on data request reliability, UX clarity, and scalable architecture. Enhanced test coverage and release hygiene to support faster iteration.
December 2025
57 Commits • 25 Features
Dec 1, 2025December 2025 - stjude/proteinpaint: Delivered major visualization enhancements and architectural improvements that strengthen analytical capabilities, reliability, and developer productivity. Key features include Wilcoxon-based box plot route, length-based rendering, and association tests integration across box plots and client display; Bar Chart length control and tooltip refinements; MVVM-driven refactor enabling charts response and improved data mapping; plus quality improvements (TypeScript build fix, UI flicker fix, release notes and docs) and testing improvements (ListSamples in shared directory, box plot tests updates).
57 Commits • 25 Features
Dec 1, 2025December 2025 - stjude/proteinpaint: Delivered major visualization enhancements and architectural improvements that strengthen analytical capabilities, reliability, and developer productivity. Key features include Wilcoxon-based box plot route, length-based rendering, and association tests integration across box plots and client display; Bar Chart length control and tooltip refinements; MVVM-driven refactor enabling charts response and improved data mapping; plus quality improvements (TypeScript build fix, UI flicker fix, release notes and docs) and testing improvements (ListSamples in shared directory, box plot tests updates).
December 2025
November 2025
59 Commits • 22 Features
Nov 1, 2025November 2025 (2025-11) monthly summary for stjude/proteinpaint focused on reliability, analytics, and plotting enhancements in the single-cell & differential expression workflows. Highlights include robust error handling and DEResponse alignment in the DE route, a hands-on DA singleCellCellType volcano workflow with prototype, enablement, and UI/plot enhancements, and extensive plotting improvements with scatter controls and axis configuration. Substantial code quality, typing, and maintainability work alongside data-model and UI enrichments to improve developer productivity and business value.
November 2025
59 Commits • 22 Features
Nov 1, 2025November 2025 (2025-11) monthly summary for stjude/proteinpaint focused on reliability, analytics, and plotting enhancements in the single-cell & differential expression workflows. Highlights include robust error handling and DEResponse alignment in the DE route, a hands-on DA singleCellCellType volcano workflow with prototype, enablement, and UI/plot enhancements, and extensive plotting improvements with scatter controls and axis configuration. Substantial code quality, typing, and maintainability work alongside data-model and UI enrichments to improve developer productivity and business value.
October 2025
5 Commits • 1 Features
Oct 1, 2025October 2025 monthly summary for stjude/proteinpaint: Delivered enhancements to support robust data visualization with an emphasis on scatter plots and data integrity. Implemented a scalable Scatter Plot Data API and processing pipeline, including new routes and TypeScript typings, enabling generation and retrieval of scatter data by genome, dataset, and visual mapping parameters. Replaced legacy termdb.scatter by a new route, cleaned up imports, and removed outdated files to improve maintainability. Fixed a critical table sorting issue for numeric values stored as strings and added unit tests to prevent regressions. These changes collectively enhance analytics capabilities, reduce user friction, and strengthen code quality for sustained business value.
5 Commits • 1 Features
Oct 1, 2025October 2025 monthly summary for stjude/proteinpaint: Delivered enhancements to support robust data visualization with an emphasis on scatter plots and data integrity. Implemented a scalable Scatter Plot Data API and processing pipeline, including new routes and TypeScript typings, enabling generation and retrieval of scatter data by genome, dataset, and visual mapping parameters. Replaced legacy termdb.scatter by a new route, cleaned up imports, and removed outdated files to improve maintainability. Fixed a critical table sorting issue for numeric values stored as strings and added unit tests to prevent regressions. These changes collectively enhance analytics capabilities, reduce user friction, and strengthen code quality for sustained business value.
October 2025
September 2025
38 Commits • 14 Features
Sep 1, 2025September 2025 performance summary for stjude/proteinpaint focused on delivering a scalable genome typing model, richer plotting capabilities, and robust UI/UX improvements that drive data exploration and maintainability. Major milestones include a comprehensive Genome Types Refactor, a plotting infrastructure overhaul with PlotBase and RxComponentInner, and substantial robustness and quality improvements across the data layer and UI. This work lays groundwork for advanced visual analyses (subplots, grin2, WSI components) and supports operational needs like retraining workflows, release hygiene, and improved documentation. Overall, the month delivered measurable business value through cleaner architecture, enhanced visualization quality, and increased developer and user productivity.
September 2025
38 Commits • 14 Features
Sep 1, 2025September 2025 performance summary for stjude/proteinpaint focused on delivering a scalable genome typing model, richer plotting capabilities, and robust UI/UX improvements that drive data exploration and maintainability. Major milestones include a comprehensive Genome Types Refactor, a plotting infrastructure overhaul with PlotBase and RxComponentInner, and substantial robustness and quality improvements across the data layer and UI. This work lays groundwork for advanced visual analyses (subplots, grin2, WSI components) and supports operational needs like retraining workflows, release hygiene, and improved documentation. Overall, the month delivered measurable business value through cleaner architecture, enhanced visualization quality, and increased developer and user productivity.
August 2025
1 Commits • 1 Features
Aug 1, 2025Month: 2025-08 — Focused on streamlining user experience and reducing unnecessary data transfer in the protein visualization suite. No new bug fix commits were recorded in this window; the month centered on feature cleanup and UI simplification within stjude/proteinpaint.
1 Commits • 1 Features
Aug 1, 2025Month: 2025-08 — Focused on streamlining user experience and reducing unnecessary data transfer in the protein visualization suite. No new bug fix commits were recorded in this window; the month centered on feature cleanup and UI simplification within stjude/proteinpaint.
August 2025
July 2025
20 Commits • 4 Features
Jul 1, 2025July 2025: Focused on reliability, maintainability, and user experience for the Disco feature in stjude/proteinpaint. Delivered documentation refresh and UI defaults to improve onboarding and error visibility; hardened settings handling and ensured settings apply during disco initialization; introduced multi-checkbox mass-control improvements with a robust check/uncheck all option and sensible defaults (including NONE) to reduce misconfiguration; and completed extensive testing and quality improvements to stabilize the codebase. These changes reduce onboarding time, lower support burden due to flaky init, and provide a more predictable configuration experience for users and developers. Technologies/skills demonstrated include Python/JS code cleanup, test-driven development, unit/integration testing, UI layout improvements, default wiring, and documentation.
July 2025
20 Commits • 4 Features
Jul 1, 2025July 2025: Focused on reliability, maintainability, and user experience for the Disco feature in stjude/proteinpaint. Delivered documentation refresh and UI defaults to improve onboarding and error visibility; hardened settings handling and ensured settings apply during disco initialization; introduced multi-checkbox mass-control improvements with a robust check/uncheck all option and sensible defaults (including NONE) to reduce misconfiguration; and completed extensive testing and quality improvements to stabilize the codebase. These changes reduce onboarding time, lower support burden due to flaky init, and provide a more predictable configuration experience for users and developers. Technologies/skills demonstrated include Python/JS code cleanup, test-driven development, unit/integration testing, UI layout improvements, default wiring, and documentation.
June 2025
15 Commits • 5 Features
Jun 1, 2025June 2025: Delivered key frontend visualization improvements, strengthened data validation, and enhanced UX, with foundational testing scaffolding. Notable work includes 3D single-cell rendering refinements, CNV heatmap color scaling, server-side validation enhancements, and UI clarity updates, plus initial LohArcMapper tests setting the stage for CI.
15 Commits • 5 Features
Jun 1, 2025June 2025: Delivered key frontend visualization improvements, strengthened data validation, and enhanced UX, with foundational testing scaffolding. Notable work includes 3D single-cell rendering refinements, CNV heatmap color scaling, server-side validation enhancements, and UI clarity updates, plus initial LohArcMapper tests setting the stage for CI.
June 2025
May 2025
31 Commits • 11 Features
May 1, 2025May 2025 monthly summary for stjude/proteinpaint focused on delivering user-facing features, stabilizing data handling, and strengthening the codebase and CI/testing.
May 2025
31 Commits • 11 Features
May 1, 2025May 2025 monthly summary for stjude/proteinpaint focused on delivering user-facing features, stabilizing data handling, and strengthening the codebase and CI/testing.
April 2025
61 Commits • 21 Features
Apr 1, 2025April 2025 (stjude/proteinpaint): Focused on reliability, usability, and parameter governance across UI, visualization, and data analysis workflows. Delivered safeguards for analytical parameters, expanded UI capabilities, and strengthened test coverage to ensure stable releases and clearer user guidance.
61 Commits • 21 Features
Apr 1, 2025April 2025 (stjude/proteinpaint): Focused on reliability, usability, and parameter governance across UI, visualization, and data analysis workflows. Delivered safeguards for analytical parameters, expanded UI capabilities, and strengthened test coverage to ensure stable releases and clearer user guidance.
April 2025
March 2025
115 Commits • 38 Features
Mar 1, 2025March 2025 performance summary for stjude/proteinpaint focused on stabilizing user workflows, strengthening maintainability, and expanding data visualization capabilities. Delivered robust UI/UX improvements, type-safety refinements, and broader test coverage to accelerate safe releases and improve user insight.
March 2025
115 Commits • 38 Features
Mar 1, 2025March 2025 performance summary for stjude/proteinpaint focused on stabilizing user workflows, strengthening maintainability, and expanding data visualization capabilities. Delivered robust UI/UX improvements, type-safety refinements, and broader test coverage to accelerate safe releases and improve user insight.
February 2025
66 Commits • 23 Features
Feb 1, 2025February 2025 performance summary for stjude/proteinpaint: Delivered a differential analysis workflow backbone, strengthened stability across analytics, and accelerated business value through UI and reliability improvements. The month focused on enabling differential expression analysis, hardening error handling, stabilizing correlation visuals, enhancing plot interactions, and improving code quality and documentation.
66 Commits • 23 Features
Feb 1, 2025February 2025 performance summary for stjude/proteinpaint: Delivered a differential analysis workflow backbone, strengthened stability across analytics, and accelerated business value through UI and reliability improvements. The month focused on enabling differential expression analysis, hardening error handling, stabilizing correlation visuals, enhancing plot interactions, and improving code quality and documentation.
February 2025
January 2025
133 Commits • 48 Features
Jan 1, 2025January 2025 for stjude/proteinpaint focused on delivering high value features, improving data clarity, and boosting stability and maintainability to accelerate decision making and future refactors. Key features delivered include disco gene and mutation tooltip improvements with removal of CNV capping from the disco legend, removal of duplicated CNV values in disco mutation tooltips, and ongoing formatting refinements for the disco gene tooltip. Significant box plot enhancements were implemented including a filter option for the label menu, robust numeric term handling, a new smallest to highest median ordering control, reuse of term1 label logic, improved tooltips, and integration tests for user settings. The TypeScript migration and typing enhancements were progressed by migrating dom/numericRangeInput to TypeScript, expanding typing across components, introducing a condensed range type and making attributes optional where appropriate. Release notes and documentation were updated to reflect these changes. Major bugs fixed include the dark mode download image issue, improved resilience via try/catch encapsulation, and rendering alignment improvements with server responses. Overall impact includes clearer data interpretation, faster exploratory analysis, increased stability in production, and a stronger foundation for safe future refactors. Technologies and skills demonstrated include TypeScript migration and typing discipline, front end charting and UI polish (box plot, violin, corrVolcano), test automation and CI readiness, and robust error handling.
January 2025
133 Commits • 48 Features
Jan 1, 2025January 2025 for stjude/proteinpaint focused on delivering high value features, improving data clarity, and boosting stability and maintainability to accelerate decision making and future refactors. Key features delivered include disco gene and mutation tooltip improvements with removal of CNV capping from the disco legend, removal of duplicated CNV values in disco mutation tooltips, and ongoing formatting refinements for the disco gene tooltip. Significant box plot enhancements were implemented including a filter option for the label menu, robust numeric term handling, a new smallest to highest median ordering control, reuse of term1 label logic, improved tooltips, and integration tests for user settings. The TypeScript migration and typing enhancements were progressed by migrating dom/numericRangeInput to TypeScript, expanding typing across components, introducing a condensed range type and making attributes optional where appropriate. Release notes and documentation were updated to reflect these changes. Major bugs fixed include the dark mode download image issue, improved resilience via try/catch encapsulation, and rendering alignment improvements with server responses. Overall impact includes clearer data interpretation, faster exploratory analysis, increased stability in production, and a stronger foundation for safe future refactors. Technologies and skills demonstrated include TypeScript migration and typing discipline, front end charting and UI polish (box plot, violin, corrVolcano), test automation and CI readiness, and robust error handling.
December 2024
65 Commits • 15 Features
Dec 1, 2024December 2024 for stjude/proteinpaint focused on expanding test coverage, refining numeric display, and enhancing color-scale/configurability to deliver clearer, faster, and more reliable visualizations. Key outcomes include expanded test coverage (TVS density unit tests), numeric formatting enhancements (RoundValueAuto scientific notation option), color-scale improvements with percentile-based outlier removal and tests, Disco color-scale/CNV UX enhancements, and GDC MAF data enrichment. These efforts improve data accuracy, reduce user confusion, and accelerate release readiness.
65 Commits • 15 Features
Dec 1, 2024December 2024 for stjude/proteinpaint focused on expanding test coverage, refining numeric display, and enhancing color-scale/configurability to deliver clearer, faster, and more reliable visualizations. Key outcomes include expanded test coverage (TVS density unit tests), numeric formatting enhancements (RoundValueAuto scientific notation option), color-scale improvements with percentile-based outlier removal and tests, Disco color-scale/CNV UX enhancements, and GDC MAF data enrichment. These efforts improve data accuracy, reduce user confusion, and accelerate release readiness.
December 2024
November 2024
56 Commits • 23 Features
Nov 1, 2024November 2024 monthly summary for stjude/proteinpaint: Delivered meaningful features to enhance UX, reliability, and maintainability; fixed critical rendering issues; strengthened typing and modularization; and laid groundwork for future interactive plotting enhancements.
November 2024
56 Commits • 23 Features
Nov 1, 2024November 2024 monthly summary for stjude/proteinpaint: Delivered meaningful features to enhance UX, reliability, and maintainability; fixed critical rendering issues; strengthened typing and modularization; and laid groundwork for future interactive plotting enhancements.
Activity
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Quality Metrics
Correctness89.8%
Maintainability88.0%
Architecture85.2%
Performance84.4%
AI Usage22.2%
Skills & Technologies
Programming Languages
HTMLJSONJavaScriptMarkdownNonePythonRTextTypeScriptplaintext
Technical Skills
3D Graphics3D Rendering3D VisualizationAI integrationAPI DesignAPI DevelopmentAPI IntegrationAPI designAPI developmentAPI integrationBack End DevelopmentBackend DevelopmentCI/CDCSSCSS Grid
Repositories Contributed To
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