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CLAUDE

CLAUDE.md — AI Context File

This file is read by Claude Code at every session startup. Keep it updated as your system evolves.

Who You Are

Name: Jonas Location: Seattle, WA Language: English

What you do: Molecular biology student at UW with a minor in neurocomputation and engineering. Working on research projects, Claude Code and OpenClaw workflows, automation tools, and applications for labs, internships, and jobs. Also building personal business(es) on the side.

Current focus: Optimizing workflow systems and building a personal brand — a public-facing website/directory and a portfolio of coding projects to showcase to labs, employers, and the world.

Your IPARAG System

This vault is organized using the IPARAG method:

  • 00 - INBOX: Capture point. Everything unprocessed lands here. Process to zero regularly.
  • 01 - PROJECTS: Time-bound outcomes with a clear finish line. Has a deadline? It goes here.
    • In Progress/ — active projects
    • On Hold/ — paused projects
  • 02 - AREAS: Ongoing responsibilities with no end date. Life domains you maintain.
  • 03 - RESOURCES: Reference material, templates, guides, SOPs.
  • 04 - ARCHIVES: Completed projects and past content.
  • 05 - GALAXY: Your Zettelkasten — permanent notes, one concept per note, flat file structure.

Routing rule: when unsure where something goes, ask: "what am I going to do with this?" not "what topic is this about?"

Your Active Projects

  • Personal Website / Directory — Build and launch a public-facing site showcasing projects, research, and brand. Finish line: live and shareable.
  • Coding Portfolio — A set of polished, documented projects demonstrating skills in automation, bio-computation, and tooling. Finish line: ready to show labs and employers.
  • Workflow Optimization — Systematize daily research, coding, and knowledge workflows using Claude Code, OpenClaw, and this vault.

Your Life Areas

  • Research — UW molecular biology research projects and lab work
  • School — Coursework, assignments, and academic obligations at UW
  • Neurocomputation — Minor coursework and projects at the intersection of computation and neuroscience
  • Business — Personal business ideas, projects, and ventures in progress
  • Health — Physical and mental wellbeing tracking
  • Finances — Financial tracking and planning
  • Career — Lab applications, internship hunting, job prep, networking

Your Galaxy (Zettelkasten)

The Galaxy is your permanent knowledge base. Flat file structure — no subfolders.

  • One note = one concept (atomicity)
  • Only synthesized thinking — no copy-pasted content
  • Notes connected via wikilinks [[Note Title]]
  • Use the Tag Taxonomy in 05 - GALAXY/Tag Taxonomy.md for consistent tagging

Note maturation path: Literature Note → synthesis → Permanent Note

Writing Style and Voice

To be calibrated from Jonas's class notes once added to the vault. Claude will analyze and update this section.

Working defaults until style is established:

  • Concise and direct. No filler.
  • First person (I), not third person.
  • Short paragraphs. Bullets over walls of text.
  • No AI-sounding transitions ("Furthermore", "In conclusion", "It's worth noting").

Rules and Preferences

  • Always write in English.
  • When creating Galaxy notes, use the permanent note format from 03 - RESOURCES/Zettelkasten Templates/Permanent Notes Template.md.
  • When routing new files, ask before placing anything in an area not yet confirmed.
  • Writing style will be calibrated once class notes are added to the vault — update this section when that happens.
  • Update this CLAUDE.md whenever a new rule, preference, or project is established.
  • Update memory/MEMORY.md at the end of each significant session.

How to Keep This File Updated

At the end of any significant session, ask Claude:

"Update CLAUDE.md and memory to reflect what we did today."

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