bioshape-analysis/blog
Oct 2024 – Dec 2024
2 Months active
Languages Used
MarkdownBibTeXJuliaLaTeXPythonQMDQuartoSQL
Technical Skills
Data ScienceMachine LearningTechnical WritingAcademic PublishingData AnalysisData Visualization
Forest Kobayashi
PROFILE
Forest Kobayashi
Worked on the bioshape-analysis/blog repository to develop and enhance an educational blog post focused on penalized principal curves for trajectory inference in cryo-EM data. The work combined rigorous technical writing with mathematical modeling to motivate the method using a hexagonal billiards example, contrast it with regression, and present the mathematical formulation. Enhancements included expanded data visualizations such as Voronoi diagrams and U-bias figures, as well as improved media assets and bibliographic updates. Leveraged Python and Julia for data analysis and visualization, and used LaTeX for documentation. The resulting content improved clarity, reproducibility, and provided a reusable reference for future algorithm development.
Overall Statistics
Feature vs Bugs
100%Features
Repository Contributions
8Total
Bugs
0
Commits
8
Features
2
Lines of code
2,961
Activity Months2
Your Network
18 peopleSame Organization
@hmc.edu4
Shared Repositories
14
Work History
December 2024
7 Commits • 1 Features
Dec 1, 2024December 2024 monthly summary for bioshape-analysis/blog: Implemented major enhancements to the Principal curves blog post, including a Jp computation overview and expanded visuals (Voronoi diagrams, U-bias figures) with updated figures and new media assets. Completed metadata corrections (front matter and date), bibliographic updates, and finalized media (final frame, output movie). These changes improve clarity, reproducibility, and reader engagement for the principal curves content. Delivered through a targeted set of commits that tracked each enhancement and fix.
7 Commits • 1 Features
Dec 1, 2024December 2024 monthly summary for bioshape-analysis/blog: Implemented major enhancements to the Principal curves blog post, including a Jp computation overview and expanded visuals (Voronoi diagrams, U-bias figures) with updated figures and new media assets. Completed metadata corrections (front matter and date), bibliographic updates, and finalized media (final frame, output movie). These changes improve clarity, reproducibility, and reader engagement for the principal curves content. Delivered through a targeted set of commits that tracked each enhancement and fix.
December 2024
October 2024
1 Commits • 1 Features
Oct 1, 2024October 2024 monthly summary for bioshape-analysis/blog: Key feature delivered was the publication of an Educational Blog Post titled "Principal Curves for Trajectory Inference in Cryo-EM". The post motivates penalized principal curves with a hexagonal billiards example, contrasts the method with regression, presents the mathematical formulation of penalized principal curves, and includes a project proposal for adapting numerical algorithms. No major bugs fixed this month for this repository. Impact includes enhanced knowledge diffusion, a clear reference for future algorithm development, and a foundation for cross-team discussions on trajectory inference in cryo-EM. Demonstrated skills include rigorous technical writing, mathematical modeling, and proposal development for algorithmic work.
October 2024
1 Commits • 1 Features
Oct 1, 2024October 2024 monthly summary for bioshape-analysis/blog: Key feature delivered was the publication of an Educational Blog Post titled "Principal Curves for Trajectory Inference in Cryo-EM". The post motivates penalized principal curves with a hexagonal billiards example, contrasts the method with regression, presents the mathematical formulation of penalized principal curves, and includes a project proposal for adapting numerical algorithms. No major bugs fixed this month for this repository. Impact includes enhanced knowledge diffusion, a clear reference for future algorithm development, and a foundation for cross-team discussions on trajectory inference in cryo-EM. Demonstrated skills include rigorous technical writing, mathematical modeling, and proposal development for algorithmic work.
Activity
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Quality Metrics
Correctness90.0%
Maintainability90.0%
Architecture90.0%
Performance82.6%
AI Usage20.0%
Skills & Technologies
Programming Languages
BibTeXJuliaLaTeXMarkdownPythonQMDQuartoSQL
Technical Skills
Academic PublishingData AnalysisData ScienceData VisualizationDocumentationGPU ComputingMachine LearningMathematical ModelingNumerical AnalysisNumerical MethodsScientific ComputingTechnical Writing
Repositories Contributed To
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