ihmeuw/vivarium_research
Dec 2024 – Jul 2026
18 Months active
Languages Used
PythonYAMLreStructuredTextrstGitGraphvizJSONJupyter Notebook
Technical Skills
CI/CDDevOpsDocumentationPython Environment ManagementSphinxCI/CD Configuration
Zeb Burke-Conte
PROFILE
Zeb Burke-conte
Over 18 months, contributed to ihmeuw/vivarium_research by building and refining simulation modeling infrastructure for global health and epidemiology research. Developed and maintained robust documentation systems using Python, Sphinx, and GitHub Actions, enabling reproducible model development and streamlined onboarding. Enhanced model validation and verification processes, introduced automated CI/CD pipelines, and improved data analysis workflows for maternal and neonatal health models. Addressed complex modeling challenges through technical writing, dependency management, and integration of AI-driven analytics. The work emphasized clarity, maintainability, and traceability, resulting in improved model accuracy, faster iteration cycles, and greater transparency for both developers and research stakeholders.
Overall Statistics
Feature vs Bugs
80%Features
Repository Contributions
154Total
Bugs
11
Commits
154
Features
44
Lines of code
730,231
Activity Months18
Your Network
142 peopleSame Organization
@uw.edu132
Shared Repositories
10
Abraham FlaxmanMember
Abraham FlaxmanMember
Jim AlbrightMember
Ali BowmanMember
Syl LutzeMember
Sylvia LutzeMember
Sylvia LutzeMember
Nathaniel Blair-StahnMember
Alix PletcherMember
Work History
July 2026
2 Commits • 1 Features
Jul 1, 2026July 2026: Strengthened documentation and validation processes in ihmeuw/vivarium_research to improve reliability, auditability, and release readiness. Delivered V&V tracking for the neonatal mortality model, recorded regression testing for model 36.1, and refreshed the validation task table to reflect current tasks. Updated run descriptions to include PAF bugfixes from model 33.1 and clarify the scope of PPH/APH updates. Included commit traceability for changes (d1e8e4ecc80d79f2523a158bd1b8053efaa1c70e; 5bbf2c419654b36f041bc1bee7a60e84ea6daef9). Business value: improved validation coverage, clearer documentation, and faster onboarding for model updates.
2 Commits • 1 Features
Jul 1, 2026July 2026: Strengthened documentation and validation processes in ihmeuw/vivarium_research to improve reliability, auditability, and release readiness. Delivered V&V tracking for the neonatal mortality model, recorded regression testing for model 36.1, and refreshed the validation task table to reflect current tasks. Updated run descriptions to include PAF bugfixes from model 33.1 and clarify the scope of PPH/APH updates. Included commit traceability for changes (d1e8e4ecc80d79f2523a158bd1b8053efaa1c70e; 5bbf2c419654b36f041bc1bee7a60e84ea6daef9). Business value: improved validation coverage, clearer documentation, and faster onboarding for model updates.
July 2026
June 2026
4 Commits • 2 Features
Jun 1, 2026June 2026 monthly summary for ihmeuw/vivarium_research: Established foundational documentation infrastructure and version-tracking enhancements to improve reproducibility, governance, and onboarding. Implemented automated build pipelines for docs and expanded run-request documentation for the vivarium_mncnh_portfolio.
June 2026
4 Commits • 2 Features
Jun 1, 2026June 2026 monthly summary for ihmeuw/vivarium_research: Established foundational documentation infrastructure and version-tracking enhancements to improve reproducibility, governance, and onboarding. Implemented automated build pipelines for docs and expanded run-request documentation for the vivarium_mncnh_portfolio.
May 2026
4 Commits • 2 Features
May 1, 2026May 2026 summary for ihmeuw/vivarium_research: Executed a major documentation and data-modeling overhaul to improve maintainability, clarity, and data fidelity. Delivered a complete APH/PPH separation, standardized postpartum period definition to 39 weeks, and updated contributor guidelines; enhanced modeling notes for postpartum contexts. Updated hemorrhage data to the GBD 2023 crosswalk with age-specific predictions and explicit uncertainty measures to align with the latest burden estimates.
4 Commits • 2 Features
May 1, 2026May 2026 summary for ihmeuw/vivarium_research: Executed a major documentation and data-modeling overhaul to improve maintainability, clarity, and data fidelity. Delivered a complete APH/PPH separation, standardized postpartum period definition to 39 weeks, and updated contributor guidelines; enhanced modeling notes for postpartum contexts. Updated hemorrhage data to the GBD 2023 crosswalk with age-specific predictions and explicit uncertainty measures to align with the latest burden estimates.
May 2026
April 2026
9 Commits • 2 Features
Apr 1, 2026Month: 2026-04 — Concise monthly summary focusing on business value and technical achievements for ihmeuw/vivarium_research. Delivered two major feature areas, improved documentation and validation traceability, and refined anemia YLDs modeling to enhance accuracy and reproducibility.
April 2026
9 Commits • 2 Features
Apr 1, 2026Month: 2026-04 — Concise monthly summary focusing on business value and technical achievements for ihmeuw/vivarium_research. Delivered two major feature areas, improved documentation and validation traceability, and refined anemia YLDs modeling to enhance accuracy and reproducibility.
March 2026
5 Commits • 1 Features
Mar 1, 2026March 2026 monthly summary for ihmeuw/vivarium_research: Delivered key enhancements to anemia modeling within the maternal health track, improving both analytics and reproducibility. Implemented an observer to track anemia person-time across maternal age groups during pregnancy and postpartum, and introduced anemia severity stratification in Years Lived with Disability (YLDs) to enable more granular outcome analysis. Completed the validation and model management work for anemia YLD modeling, including merging previous model versions, updating V&V tables, and enhancing documentation with related links. Addressed build issues to stabilize the modeling pipeline and updated V&V documentation accordingly.
5 Commits • 1 Features
Mar 1, 2026March 2026 monthly summary for ihmeuw/vivarium_research: Delivered key enhancements to anemia modeling within the maternal health track, improving both analytics and reproducibility. Implemented an observer to track anemia person-time across maternal age groups during pregnancy and postpartum, and introduced anemia severity stratification in Years Lived with Disability (YLDs) to enable more granular outcome analysis. Completed the validation and model management work for anemia YLD modeling, including merging previous model versions, updating V&V tables, and enhancing documentation with related links. Addressed build issues to stabilize the modeling pipeline and updated V&V documentation accordingly.
March 2026
February 2026
4 Commits • 1 Features
Feb 1, 2026February 2026 (ihmeuw/vivarium_research): Delivered comprehensive documentation improvements and introduced a reusable build workflow for Vivarium docs. Key work included expanding hemoglobin exposure documentation for GBD 2023 (pregnant populations; data storage for modelable entities), clarifying time handling in the MNCNH simulation, correcting an AI-generated error in the concept model document link, and creating new documentation files with a build workflow and .gitignore to improve clarity and maintainability. Notable commits include 123c1203e50feca66c2d5ac959e9386f3dcddc86 (Add more notes about hemoglobin exposure in GBD 2023), 4563accee78d2b17a87df70315577e76f47da7c9 (Document approach to time in MNCNH sim), 05ba4bc7d64699fed3d3642e539be2ed33309c04 (Correct AI hallucination), 4cc62211bd23d2a179255a324602ffc6b611119b (Couple more tweaks).
February 2026
4 Commits • 1 Features
Feb 1, 2026February 2026 (ihmeuw/vivarium_research): Delivered comprehensive documentation improvements and introduced a reusable build workflow for Vivarium docs. Key work included expanding hemoglobin exposure documentation for GBD 2023 (pregnant populations; data storage for modelable entities), clarifying time handling in the MNCNH simulation, correcting an AI-generated error in the concept model document link, and creating new documentation files with a build workflow and .gitignore to improve clarity and maintainability. Notable commits include 123c1203e50feca66c2d5ac959e9386f3dcddc86 (Add more notes about hemoglobin exposure in GBD 2023), 4563accee78d2b17a87df70315577e76f47da7c9 (Document approach to time in MNCNH sim), 05ba4bc7d64699fed3d3642e539be2ed33309c04 (Correct AI hallucination), 4cc62211bd23d2a179255a324602ffc6b611119b (Couple more tweaks).
January 2026
1 Commits
Jan 1, 2026Month: 2026-01 — Focused on refining verification & validation (V&V) processes for ihmeuw/vivarium_research. Delivered a V&V tracking update and ensured model output alignment with gestational age and neonatal mortality adjustments, addressing discrepancies from prior versions. The changes enhance validation readiness and reduce risk in releases.
1 Commits
Jan 1, 2026Month: 2026-01 — Focused on refining verification & validation (V&V) processes for ihmeuw/vivarium_research. Delivered a V&V tracking update and ensured model output alignment with gestational age and neonatal mortality adjustments, addressing discrepancies from prior versions. The changes enhance validation readiness and reduce risk in releases.
January 2026
December 2025
17 Commits • 5 Features
Dec 1, 2025December 2025 monthly summary for ihmeuw/vivarium_research highlighting business value and technical achievements. Focused on delivering robust verification and validation (V&V) improvements for maternal disorders and pregnancy outcomes, refining ANC modeling, updating population parameters to reflect actual runs, and enhancing documentation to support policy-relevant modeling. Key efforts strengthened model fidelity, reduced risk of misinterpretation, and improved readiness for stakeholder decision making.
December 2025
17 Commits • 5 Features
Dec 1, 2025December 2025 monthly summary for ihmeuw/vivarium_research highlighting business value and technical achievements. Focused on delivering robust verification and validation (V&V) improvements for maternal disorders and pregnancy outcomes, refining ANC modeling, updating population parameters to reflect actual runs, and enhancing documentation to support policy-relevant modeling. Key efforts strengthened model fidelity, reduced risk of misinterpretation, and improved readiness for stakeholder decision making.
November 2025
11 Commits • 5 Features
Nov 1, 2025Month: 2025-11 — ihmeuw/vivarium_research. Overview: Delivered key features, validated results, and strengthened model governance to support policy-relevant insights. Focused on AI ultrasound analyses, mortality validations, and robust run/versioning/documentation. Key features delivered include AI ultrasound sensitivity analysis with gestational-age error adjustment; AI ultrasound mitigation documentation; stillbirth estimates upgrade and expanded neonatal mortality validation in model runs; model run verification, versioning, and documentation improvements; and hemoglobin model refactor with updated documentation/simulation scenarios. Major bugs fixed/quality improvements include run tracking and versioning clarifications (avoiding premature numbering), documentation of skipped numbers, and a corrected hemoglobin model run. Impact: improved accuracy and validation coverage for stillbirth and neonatal mortality within model runs; greater reproducibility and governance through enhanced V&V, versioning, and run-tracking documentation; clearer AI ultrasound transparency for decision-makers. Technologies/skills demonstrated: model run orchestration and versioned pipelines, sensitivity analysis design, data validation, documentation standards, V&V procedures, and code refactoring for consistency.
11 Commits • 5 Features
Nov 1, 2025Month: 2025-11 — ihmeuw/vivarium_research. Overview: Delivered key features, validated results, and strengthened model governance to support policy-relevant insights. Focused on AI ultrasound analyses, mortality validations, and robust run/versioning/documentation. Key features delivered include AI ultrasound sensitivity analysis with gestational-age error adjustment; AI ultrasound mitigation documentation; stillbirth estimates upgrade and expanded neonatal mortality validation in model runs; model run verification, versioning, and documentation improvements; and hemoglobin model refactor with updated documentation/simulation scenarios. Major bugs fixed/quality improvements include run tracking and versioning clarifications (avoiding premature numbering), documentation of skipped numbers, and a corrected hemoglobin model run. Impact: improved accuracy and validation coverage for stillbirth and neonatal mortality within model runs; greater reproducibility and governance through enhanced V&V, versioning, and run-tracking documentation; clearer AI ultrasound transparency for decision-makers. Technologies/skills demonstrated: model run orchestration and versioned pipelines, sensitivity analysis design, data validation, documentation standards, V&V procedures, and code refactoring for consistency.
November 2025
October 2025
9 Commits • 3 Features
Oct 1, 2025October 2025 monthly summary for ihmeuw/vivarium_research focusing on documentation and release workflow improvements. Key work included: (1) Documentation improvements for the MNCNH portfolio, with standardized terminology around hemoglobin measurements in pregnancy, removal of outdated notes, and clearer diagrams (drawio) to support understanding and onboarding. (2) CI/CD email notification enhancements to improve build failure visibility, including an automated email on failure, refined trigger rules, and updated email subject/body for clarity. (3) Release management: version bump to prepare for the October release, ensuring traceability and proper packaging without functional changes.
October 2025
9 Commits • 3 Features
Oct 1, 2025October 2025 monthly summary for ihmeuw/vivarium_research focusing on documentation and release workflow improvements. Key work included: (1) Documentation improvements for the MNCNH portfolio, with standardized terminology around hemoglobin measurements in pregnancy, removal of outdated notes, and clearer diagrams (drawio) to support understanding and onboarding. (2) CI/CD email notification enhancements to improve build failure visibility, including an automated email on failure, refined trigger rules, and updated email subject/body for clarity. (3) Release management: version bump to prepare for the October release, ensuring traceability and proper packaging without functional changes.
September 2025
18 Commits • 2 Features
Sep 1, 2025September 2025 monthly summary focusing on key accomplishments, major bugs fixed, and overall impact. The team delivered essential modeling improvements and documentation enhancements across ihmeuw/vivarium_research, with strong emphasis on business value, reproducibility, and cross-repo consistency.
18 Commits • 2 Features
Sep 1, 2025September 2025 monthly summary focusing on key accomplishments, major bugs fixed, and overall impact. The team delivered essential modeling improvements and documentation enhancements across ihmeuw/vivarium_research, with strong emphasis on business value, reproducibility, and cross-repo consistency.
September 2025
August 2025
9 Commits • 1 Features
Aug 1, 2025In August 2025, delivered documentation-driven validation and visualization enhancements for the Concept Model within ihmeuw/vivarium_research, strengthening V&V readiness and stakeholder comprehension. Consolidated updates across the concept model and simulations, added V&V criteria and results for models 13.2 and 13.3, clarified initialization strategy for the same-number-of-simulants approach in preterm birth calculations, and improved MNCNH Portfolio documentation with scope, objectives, and component explanations. Also improved chart interpretation guidance to avoid misinterpretation, and completed minor formatting/typo fixes to enhance usability.
August 2025
9 Commits • 1 Features
Aug 1, 2025In August 2025, delivered documentation-driven validation and visualization enhancements for the Concept Model within ihmeuw/vivarium_research, strengthening V&V readiness and stakeholder comprehension. Consolidated updates across the concept model and simulations, added V&V criteria and results for models 13.2 and 13.3, clarified initialization strategy for the same-number-of-simulants approach in preterm birth calculations, and improved MNCNH Portfolio documentation with scope, objectives, and component explanations. Also improved chart interpretation guidance to avoid misinterpretation, and completed minor formatting/typo fixes to enhance usability.
July 2025
13 Commits • 2 Features
Jul 1, 2025Concise monthly summary for July 2025 focusing on key deliverables, fixes, and impact for ihmeuw/vivarium_research. Emphasizes business value, technical achievements, and demonstrated skills.
13 Commits • 2 Features
Jul 1, 2025Concise monthly summary for July 2025 focusing on key deliverables, fixes, and impact for ihmeuw/vivarium_research. Emphasizes business value, technical achievements, and demonstrated skills.
July 2025
May 2025
1 Commits • 1 Features
May 1, 2025May 2025 monthly summary for ihmeuw/vivarium_research: Focused on clarifying COMO restriction rules for simulants and ensuring accurate references and links in documentation. This work improves model usage clarity and onboarding for new developers. No major bug fixes were recorded this month; efforts concentrated on documentation quality and maintainability.
May 2025
1 Commits • 1 Features
May 1, 2025May 2025 monthly summary for ihmeuw/vivarium_research: Focused on clarifying COMO restriction rules for simulants and ensuring accurate references and links in documentation. This work improves model usage clarity and onboarding for new developers. No major bug fixes were recorded this month; efforts concentrated on documentation quality and maintainability.
March 2025
25 Commits • 11 Features
Mar 1, 2025March 2025: Delivered substantive feature improvements, reliability enhancements, and documentation updates for ihmeuw/vivarium_research. Implemented a new CPAP Page Enhancement with alternative PAF derivation, enhanced fuzzy checking uncertainty, and unpinned Sphinx to enable updates. Strengthened CI operations and reproducibility by re-triggering builds and re-running CI. Completed tutorial implementation with results processing and introduced ipywidgets for improved interactivity. Expanded documentation across prevalence, covariance, unit increase language, and baseline deletion explanations, while clarifying RR/PAF semantics. Consolidated minor UI tweaks and maintained code health through targeted bug fixes and version bumps. Overall, these efforts improve model accuracy, developer velocity, and user-facing clarity, driving faster, more reliable experimentation and decision-making.
25 Commits • 11 Features
Mar 1, 2025March 2025: Delivered substantive feature improvements, reliability enhancements, and documentation updates for ihmeuw/vivarium_research. Implemented a new CPAP Page Enhancement with alternative PAF derivation, enhanced fuzzy checking uncertainty, and unpinned Sphinx to enable updates. Strengthened CI operations and reproducibility by re-triggering builds and re-running CI. Completed tutorial implementation with results processing and introduced ipywidgets for improved interactivity. Expanded documentation across prevalence, covariance, unit increase language, and baseline deletion explanations, while clarifying RR/PAF semantics. Consolidated minor UI tweaks and maintained code health through targeted bug fixes and version bumps. Overall, these efforts improve model accuracy, developer velocity, and user-facing clarity, driving faster, more reliable experimentation and decision-making.
March 2025
February 2025
7 Commits • 1 Features
Feb 1, 2025February 2025 monthly summary for ihmeuw/vivarium_research focusing on documentation work for the CPAP intervention model, risk factors, and Sphinx build stability improvements. These changes enhance user-facing documentation clarity, cross-project navigation, and CI reliability, delivering tangible business value in maintainability and user adoption.
February 2025
7 Commits • 1 Features
Feb 1, 2025February 2025 monthly summary for ihmeuw/vivarium_research focusing on documentation work for the CPAP intervention model, risk factors, and Sphinx build stability improvements. These changes enhance user-facing documentation clarity, cross-project navigation, and CI reliability, delivering tangible business value in maintainability and user adoption.
January 2025
12 Commits • 3 Features
Jan 1, 2025January 2025 — ihmeuw/vivarium_research monthly summary emphasizing key feature delivery, major fixes, impact, and demonstrated skills.
12 Commits • 3 Features
Jan 1, 2025January 2025 — ihmeuw/vivarium_research monthly summary emphasizing key feature delivery, major fixes, impact, and demonstrated skills.
January 2025
December 2024
3 Commits • 1 Features
Dec 1, 2024December 2024 monthly summary for ihmeuw/vivarium_research focusing on documentation tooling and CI runtime upgrades, with a targeted bug fix to the contributor guide. Key improvements include faster docs workflow, broader Python compatibility, and corrected contributor instructions. These changes reduce cycle times for documentation and improve onboarding for contributors.
December 2024
3 Commits • 1 Features
Dec 1, 2024December 2024 monthly summary for ihmeuw/vivarium_research focusing on documentation tooling and CI runtime upgrades, with a targeted bug fix to the contributor guide. Key improvements include faster docs workflow, broader Python compatibility, and corrected contributor instructions. These changes reduce cycle times for documentation and improve onboarding for contributors.
Activity
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Quality Metrics
Correctness91.6%
Maintainability90.6%
Architecture88.4%
Performance86.0%
AI Usage24.2%
Skills & Technologies
Programming Languages
GitGraphvizJSONJupyter NotebookMakefileMarkdownPythonRRSTSVG
Technical Skills
AI correctionAI integrationBug FixingCI/CDCI/CD ConfigurationCausal DiagramsData AnalysisData Visualization (Causal Diagrams)Dependency ManagementDevOpsDiagrammingDocumentationEpidemiologyGBD DataGit
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