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Andrew Willems

PROFILE

Andrew Willems

Over an 18-month period, contributed to the stjude/proteinpaint repository by building advanced analytics and visualization features for genomic and biomedical data. Developed robust end-to-end workflows for GRIN2 analysis, DNA methylation, and isoform expression, integrating Rust, TypeScript, and Python for scalable backend and interactive frontend components. Emphasized maintainability through extensive refactoring, comprehensive testing, and detailed documentation, while implementing caching, concurrency management, and memory profiling to optimize performance. Enhanced user experience with dynamic UI elements, high-resolution SVG and canvas rendering, and real-time feedback. The work enabled reliable, reproducible analyses and accelerated onboarding for researchers and developers working with complex datasets.

Overall Statistics

Feature vs Bugs

70%Features

Repository Contributions

811Total
Bugs
125
Commits
811
Features
286
Lines of code
131,368
Activity Months18

Your Network

46 people

Same Organization

@stjude.org
17

Work History

June 2026

39 Commits • 15 Features

Jun 1, 2026

June 2026 monthly recap for stjude/proteinpaint focusing on delivering measurable business value through performance, reliability, and data integration improvements. Highlights include feature delivery, data quality enhancements, and targeted QA efforts across GRIN2 data workflows.

May 2026

44 Commits • 21 Features

May 1, 2026

May 2026 monthly summary for stjude/proteinpaint focusing on delivered features, bug fixes, impact, and technical excellence. Highlights include caching-enabled feature work, frontend UX improvements, and architectural refactors that improve performance, reliability, and maintainability. The month also delivered release readiness artifacts and expanded testing coverage to reduce regressions.

April 2026

67 Commits • 20 Features

Apr 1, 2026

April 2026 (2026-04) monthly summary for stjude/proteinpaint focused on expanding isoform-aware analytics, strengthening code quality, and accelerating data-driven insights. Delivered tangible business value through improved data fidelity, faster pipelines, and more reliable CI/test stability, enabling scalable analyses for isoform expression and related DA workflows.

March 2026

51 Commits • 20 Features

Mar 1, 2026

March 2026 monthly summary for stjude/proteinpaint: Focused on strengthening data robustness, expanding analytical capabilities, and improving release readiness. Delivered a robust JSON resource parsing pathway, enabling explicit validation and safer integer indexing, reducing potential silent failures. Introduced initial ssGSEA support across chart types with refactoring to share common tasks, enabling consistent, scalable enrichment analyses. Implemented region-level DNA methylation analysis with a DMRCate-based backend, replacing GPDM, and added Rust/R interop testing to validate cross-language implementations. Expanded methylation analysis features, including DA app integration and promoter unit parameter support, broadening analysis scope. Improved release/test hygiene with added release notes, updated R unit tests, new test data, and promoter HDF5 validation tests, supporting reproducibility and collaboration.

February 2026

80 Commits • 30 Features

Feb 1, 2026

February 2026 (2026-02) monthly summary for stjude/proteinpaint. Focus this month was on strengthening analytics reliability, expanding visualization capabilities, and improving code quality to deliver clearer business value and maintainable software. Key features delivered: - GRIN2 Stats Overhaul and Memory Tracking: Consolidated and expanded the GRIN2 stats subsystem, simplifying outputs under a single stats object, introducing an initial lst: string[][] structure, and enabling memory usage reporting to be always-on. This improves observability and supports data-driven capacity planning. - GRIN2 Chart Type Handling Fixes: Ensured user-specified chart types in queries are respected, removed unnecessary chart types, and refined data flow to support dynamic lesion types without extra copies, improving correctness and performance. - LLM: Multiple Chart Types and Matrix Support: Enabled multiple chart types within LLM-generated summaries and refactored configuration under serverconfig.llm, with initial matrix support in the chatbot and accompanying tests. - Matrix chart type support and UMAP/t-SNE plots: Added matrix chart type support and UMAP/t-SNE visualization options with variable overlays to broaden exploratory capabilities. - Table and UI improvements: Restored original row order in Table.ts, adjusted related tests, and streamlined UI to align with updated stats table presentation. Major bugs fixed: - GRIN2 Concurrency Testing Script Removal: Deleted the concurrency test script as it was moved to another repo, reducing maintenance surface. - Matrix route logging cleanup: Removed unnecessary console logs to reduce noise in production logs. - RAG removal for figures/references/full text: Return web links only to simplify data access paths. - Code migrations and route fixes: Migrated classification/resource agents to new locations and stabilized termdb.chat2.ts workflows with TypeScript fixes. - TypeScript and route fixes: Addressed tsc errors in termdb.chat.ts route and other minor route/API cleanup to improve build stability. - Additional quality fixes: Copilot feedback addressed, scatter plot edge-case fix, and various wording/structure cleanups for reliability. Overall impact and accomplishments: - Delivered substantial improvements to analytics observability, visualization capabilities, and data-driven workflows, enabling more reliable monitoring and richer end-user insights. The introduced stat structure and robust chart/type handling enhance decision-making fidelity for researchers and product teams. Refactors and quality fixes reduced technical debt and improved maintainability across the repo. Technologies/skills demonstrated: - TypeScript/TS tooling, strong refactoring discipline, and configuration management (serverconfig.llm). - Advanced data visualization capabilities (GRIN2 charts, matrix plots, UMAP/t-SNE). - Improved test coverage and CI resilience through updated tests and cleanup.

January 2026

37 Commits • 16 Features

Jan 1, 2026

January 2026 (Month: 2026-01) — stjude/proteinpaint: Delivered GRIN2 visualization enhancements, memory and performance improvements, and code quality upgrades, enabling clearer data interpretation, scalable analyses, and faster onboarding. Highlights include a dynamic y-axis cap for Manhattan plots with parameterized binning, memory-tracking and scaling to support large lesion counts, asynchronous concurrency readiness, and comprehensive documentation and testing improvements. These changes deliver measurable business value by improving visualization accuracy, runtime efficiency, and maintainability while reducing production risk.

December 2025

62 Commits • 26 Features

Dec 1, 2025

December 2025 (stjude/proteinpaint) focused on delivering GRIN2 enhancements, stabilizing the plotting/tooltip UX, and tightening performance and code quality. Key work spanned feature delivery, bug fixes, and robust testing to drive clearer insights and reliable visualization for end users and stakeholders.

November 2025

62 Commits • 23 Features

Nov 1, 2025

November 2025 monthly summary for stjude/proteinpaint focusing on business value and technical achievements. Highlights include GRIN2 UI/state improvements, automated live-link analysis, expanded test coverage, and visualization/backend enhancements that improve reliability, user experience, and data fidelity.

October 2025

68 Commits • 18 Features

Oct 1, 2025

October 2025 (2025-10) – stjude/proteinpaint: Delivered key features across lesion tracking, GRIN2 data types, and UI/UX; fixed production issues; improved reliability and performance. Key features include lesion cap by type with unified dt cap and enhanced tracking; processing summary overhaul; GRIN2 data type support for fusion/SV with UI/backend integration and flanking size handling; dynamic SV fusion UI controls and data-type selection UI with SNVindel filtering; and background improvements including cacheFile enhancements, midpoint calculation fix, and dependency pinning. Business impact: more accurate lesion tracking, faster processing, richer data exploration, and reduced production risk.

September 2025

49 Commits • 15 Features

Sep 1, 2025

For 2025-09 (stjude/proteinpaint), delivered a series of substantial plotting and UI improvements focused on accuracy, performance, and developer productivity across the main visualization stack (SVG/Manhattan plots) with strengthening data handling and documentation. Key features delivered include a suite of SVG plotting enhancements, UI/UX improvements for gene hover, dynamic axis padding with default plot parameters, Manhattan plot integration and enhancements, and improvements in PNG/D3 rendering compatibility. In parallel, notable code quality and maintenance work included cleanup, error handling standardization, and documentation updates.

August 2025

17 Commits • 2 Features

Aug 1, 2025

In August 2025, delivered end-to-end GRIN2 processing enhancements in the stjude/proteinpaint project, establishing a robust backend API and an integrated UI for GRIN2 analysis. This work enables researchers to process GRIN2 data (SNV/Indel/CNV) with clear data-type tracking, end-to-end routes in the portal, interactive visualizations, and configurable analyses. The month also included code quality improvements and groundwork for scalable visualization and data exploration in the portal.

July 2025

25 Commits • 11 Features

Jul 1, 2025

July 2025 monthly summary focusing on GRIN2 module enhancements in stjude/proteinpaint, with emphasis on business value and technical achievements. Highlights include plotting/UI improvements, data display refinements, internal refactors to reduce technical debt, and API route groundwork to enable future integrations. The work strengthened data visibility for researchers, improved maintainability, and laid the foundation for scalable GRIN2 onboarding and reporting.

June 2025

74 Commits • 30 Features

Jun 1, 2025

June 2025 monthly summary for stjude/proteinpaint focused on user experience refresh, data integration, and performance/quality improvements that unlock faster data exploration and broader data support (CNV, MAF, GRIN2, and top-gene analyses).

May 2025

60 Commits • 21 Features

May 1, 2025

May 2025 monthly summary for stjude/proteinpaint focusing on delivering measurable business value through code quality, data modeling, and user-facing analytics. Highlights include end-to-end GRIN2 route integration, UI/visualization improvements, and tooling enhancements that increase development velocity, reliability, and release-readiness.

April 2025

32 Commits • 5 Features

Apr 1, 2025

April 2025 monthly summary for stjude/proteinpaint: Delivered time formatting standardization, HDF5-based gene expression enhancements, and migration cleanups; improved typing and test coverage; boosted reliability and performance for multi-gene queries and large datasets.

March 2025

23 Commits • 7 Features

Mar 1, 2025

March 2025 monthly summary for stjude/proteinpaint highlighting delivery of HDF5/TPM workflow enhancements and stabilization work across Rust and TypeScript components. Focused on enabling TPM data ingestion, robust data paths to the UI, and maintainable, well-documented codebase with improved validation and JSON outputs.

February 2025

6 Commits • 2 Features

Feb 1, 2025

February 2025 monthly summary for stjude/proteinpaint: Delivered reliability-focused enhancements to table exports, introduced inline barplots for key scores within table columns, and cleaned production logs by removing an unnecessary console log. These efforts improved data export integrity, in-context data interpretation, and maintainability, delivering measurable business value for researchers relying on accurate exports and clear visual cues in tables.

January 2025

15 Commits • 4 Features

Jan 1, 2025

Monthly summary for 2025-01 focusing on development work in stjude/proteinpaint. Key achievements include extensive testing, documentation improvements, and UI/visualization refinements that increase reliability and maintainability. Highlights: - DecimalPlacesUntilFirstNonZero: Documentation and tests added (docs: Add additional documentation for decimalPlacesUntilFirstNonZero tests). Commit references: 7ce408ceaa7a90372b5f2a55aaa0c4c3530eabbb; 8189c7c7f656414e1cfb28703b0f1535841d243b. - ParseRange function tests for numericRangeInput.ts: Comprehensive test suite covering exact values, ranges, decimals, negatives, whitespace, and error handling. Commit: d9b5dbf363af92ff669ab023e4175797a420670e. - Max label width utilities consolidation and tests: Centralize label width calculations, adopt type-safe getMaxLabelWidth, add client/dom utility, test maxLabelWidth, and move summary.utils to client/dom. Commits: 566032c2bd19d4186efd9f9819985f33da62ddcb; bc4cfb979112577b3c31dfa74a8e0619bb26595c; 7e1bb0a428fba5cf886cb890a8d689241697e9a0; 05c0c340d8deb3c48292b9b784d1501960885bda; d043c1b6680d96ac86aeadf1ecfd83c7d443dc00. - Color scale enhancements for sample scatter plot: New color scaling modes, improved persistence/state management, synchronization fixes, and cleanup. Commits: 512f4fdf7c8be97753e37e295edf7be78abb9d11; fa8142b5bde09a12f9ccf686fdb0e3c24da066a5; f6b3ac1604d1cf4efc05c0d920eb08c61767a8f3; 1173ce2556e85d872189cb6c9ed989147b1f7e18; 89d89a635da24c1ae7f994d05bd951782417c6f5; 7d957633f8fc6492655587217c5e6f249856f4e2; 386f2703d683a8f9ff9a72617a324d0bce5460b9. Overall impact: These contributions increase test coverage, reduce regression risk, improve visualization fidelity, and enhance maintainability. They lay groundwork for more robust releases and quicker onboarding for new contributors. Technologies/skills demonstrated: TypeScript, unit/integration testing, test-driven development, utility refactoring and consolidation, client/dom architecture shifts, and UI state management for complex visualizations.

Activity

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Quality Metrics

Correctness89.4%
Maintainability86.6%
Architecture84.8%
Performance83.8%
AI Usage27.6%

Skills & Technologies

Programming Languages

BashCSSDockerfileGitHTMLJSONJavaScriptMarkdownMatplotlibPython

Technical Skills

AI DevelopmentAI IntegrationAI configurationAI integrationAI/ML integrationAPI DesignAPI DevelopmentAPI DocumentationAPI IntegrationAPI developmentAPI integrationAPI testingBack End DevelopmentBack-end DevelopmentBackend Development

Repositories Contributed To

1 repo

Overview of all repositories you've contributed to across your timeline

stjude/proteinpaint

Jan 2025 Jun 2026
18 Months active

Languages Used

JavaScriptTypeScriptCSSHTMLJSONRustTOMLR

Technical Skills

Chart RenderingCode OptimizationCode RefactoringD3.jsData VisualizationDocumentation