#annotations

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    Occasionally, the notes on this site will be annotative notes on other folks’ works that I find interesting. Whenever possible, I’ll make these annotations public, especially when the sources are publicly available.

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    Recent Posts

    • Design of a mucin-selective protease for targeted degradation of cancer-associated mucins

      — The rubber hits the road on ColabFold! I hope that's rubber I'm smelling — although it may be the computer. A replication attempt of a protein fold figure in K. Pedram et al (2023). (7 min read)

    • An Annotated Guide to Hobbyist Protein Folding

      — Amaze (or bore) your friends and family by picking up on a hot new hobby that's all the rage — protein folding! An annotated starter to the 2021 paper "ColabFold - Making protein folding accessible to all" (8 min read)

    • Agentic Programming as Theory Building

      — Do humans have a role in software development anymore? Absolutely — but we need to rethink what it means to program. An modern review of Peter Naur's 1985 essay "Programming as Theory Building" (33 min read)

    • APL: Pattern 4; Agricultural Valleys

      — Urban development has the high ground over agricultural and ecological preservation — and it should! *A Pattern Language* annotations on Pattern 4: Agricultural Valleys (2 min read)

    • APL: Pattern 5; Lace of Country Streets

      — How dense is too dense? How sparse is too sparse? Annotations for A Pattern Language's proposals for the density of metro-adjacent country streets for agriculture, recreation, and preservation. (3 min read)

    Show 13 more posts

    • APL: Pattern 1; Independent Regions

      — Home isn't where the heart is — it's a single node on a very, very large graph. Annotations for the "Independent Regions" pattern of *A Pattern Language*. (10 min read)

    • APL: Pattern 2; The Distribution of Towns

      — How close is too close? How far is too far? *A Pattern Language* annotations related to the statistical, economic, and ecologic concerns in balancing how dense human habitats ought to be. (5 min read)

    • APL: Pattern 3; City Country Fingers

      — City, with natural stripes — or nature, with city stripes? Annotations for A Pattern Language, and tracking public opinion of where Americans want to live over the past 50 years. (4 min read)

    • APL: Pattern 0; Introduction

      — Can graphs be libertarian? Authoritarian? Annotations for the introductory portion of the 1977 book A Pattern Language. (9 min read)

    • Ants in the Neighborhood

      — Is Jane Street run by soccer-loving ants? Inconclusive. We *can* conclude that they're fans of Markov Chains, though — an invaluable tool for understanding complex data structures. (1 min read)

    • A Pattern Language, and a Beautiful Day in the Neighborhood

      — The beginning of a topological review of the 1977 urban design and architecture reference book A Pattern Language, and a journey to understand Earth's greatest graph: the Earth, itself. (12 min read)

    • Evolution and Revolution as Organizations Grow

      — Annotations for Greiner's 1972 paper "Evolution and Revolution as Organizations Grow", about the structural composition of organizations at different sizes and requirements. (12 min read)

    • Intro to Event Storming

      — Notes from learning Event Storming for domain-driven design. Thoughts on phases, color-coded chaos, and how to transition from fast pitches to full products. (6 min read)

    • LLMs: A Primer Presentation for Our Newest, Scariest Tool

      — An engineer-focused primer on the mechanisms that drive Large Language Models. Basics on how we got here, how they work, and how to use them without feeling an apocalyptic dread. (1 min read)

    • Terraform LocalStack Testing

      — $70/mo/seat? Just using live AWS may be cheaper. An evaluation of LocalStack as a testbed for Account Factory Terraform. (5 min read)

    • The Simple Economics of Open Source

      — Why do we do what we do? "Egoboo." Exploring economic models of OSS contributions beyond altruism and ego. (8 min read)

    • College Admissions and the Stability of Marriage

      — A dive into the hottest algorithm of the 1960s: Gale-Shapley matchmaking. Who knew that the mysteries of the heart could be solved with a matrix? (5 min read)

    • Utah Office Consult

      — People problems are the hardest engineering problems. A consult on thinking out-of-the-box to explain morale problems in small companies. (2 min read)

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