Section 03 — how this was built
Built with
Claude Code
NeoFlex Designer — an eight-module pipeline that turns a biological objective into an orderable, in-silico neochromosome — was designed and written end to end with Claude Code. Every figure below is read from the project's own usage tracker and git history, and checked for internal consistency, not estimated.
Token usage
usage/summary.jsonCode written
git log · numstatwc -lPython lines added per day · cumulative to 161,883
Commit history
git log · 351 commitsCommits per day · cumulative to 351
Work by area · commit-message prefix
Tools & orchestration
4,488 tool callsTool calls · top 12 of 46
Subagent runs · 105
Workflows · 83
How it was built
the working patternA queryable literature wiki seeded the design
Ideation ran on a self-hosted LLM literature wiki (AutoSci, a vendored MIT research-agent toolkit). Claude cross-linked the neochromosome, CAZyme and metabolic-engineering literature into a searchable wiki that seeded the DesignSpec and M1's evidence-backed discovery, so parts trace to real accessions and DOIs, not model recall.
Continuous waves of ~8 Opus subagents
Work was fanned out in rolling waves of roughly eight Opus subagents at a time. The tracker logged 105 subagent runs, and 99.7% of all 11,084 turns ran on Claude Opus 4.8. The history carries explicit wave13-e2e / wave17-e2e checkpoints.
A living board, auto-updated on every commit
A module status board under kanban/ tracked working / partial / missing features and test counts per module, regenerated by a git post-commit hook. It is the most-touched artifact in the repo: 73 of 351 commits carry the kanban: prefix.
Changes were gated to a go / no-go
Dedicated review, audit and go-review passes (14 commits) plus 83 workflows fed a reviews/ tree of findings, catching fabricated citations before an order package. Modules talk through 12 versioned contract: schemas validated by a deterministic harness; runs looped until the fail-closed gate cleared.
Full dashboard
04_Claude_usage_tracking04_Claude_usage_tracking/usage/summary.json (snapshot 2026-07-13T13:01Z); commit and line-of-code figures from git log over 351 commits (2026-07-14). Raw copies ship beside this page as assets/usage_summary.json and dashboard.html.