Allen Institute Nautilex 2026 Challenge Capsules

This repository documents an AI-driven implementation sprint for the Allen Institute Nautilex 2026 hackathon challenges.

The goal was simple: take the challenge prompts, build a Code Ocean capsule for each one, run them as standalone research products, review the results honestly, and iterate fast.

Over 4 days and 3 implementation / review iterations, the work was driven through Code Ocean Aqua and Claude Code:

• Aqua was used as the Code Ocean agent layer for building and running the capsules.
• Claude Code was used as the coding agent to implement and revise the capsules.
• Claude Code was also used as a critic across iterations to review outputs, identify gaps, and drive the next round of fixes.

Live Atlas

• GitHub Pages atlas:https://codeocean.github.io/challenges-capsules/
• Repo atlas source:index.html
• Repo capsule index:index.md
• Iteration 03 summary:working-capsules-summary.md

Outcome

The current repo snapshot covers 15 capsules for Challenges 02-16.

• 11 completed
• 4 partially completed
• 0 blocked

The most important outcome is not just the code. It is the combination of:

• runnable capsule implementations
• capsule-specific READMEs
• review summaries with honest limitations
• a local and hosted HTML atlas for fast navigation

What Is In This Repo

• challenge_02_* to challenge_16_*: the capsule codebases
• index.html: the main navigable atlas
• docs/: styled HTML pages for every local README and review summary
• review-challanges-iteration-03/: iteration-03 review bundle
• build-embedded-docs.mjs: rebuilds the embedded markdown bundle
• build-static-doc-pages.mjs: regenerates the static HTML doc pages

Quick Navigation

Challenge	Capsule	Status	Live README	Live Review
02	Agentic Data Harmonization	Completed	README	Review
03	Enhancer Designer	Completed	README	Review
04	Light Sheet Alignment QC	Completed	README	Review
05	Automate Your Productivity	Partial	README	Review
06	Plasmid Forge	Partial	README	Review
07	Engineering Automation	Completed	README	Review
08	Query BFF	Completed	README	Review
09	BindCrafting	Partial	README	Review
10	NeuroBase Foundation Model Evaluation	Completed	README	Review
11	ABC Atlas Literature Assistant	Completed	README	Review
12	Brain Map + BKP Assistant	Completed	README	Review
13	Croissant Pipeline	Completed	README	Review
14	Segment Intestine Villi	Completed	README	Review
15	Allen Single Cell Model Pantry	Partial	README	Review
16	SciDEX	Completed	README	Review

Fastest Way To Explore

1. Open the live atlas: https://codeocean.github.io/challenges-capsules/
2. Use the sortable top table to scan by challenge, status, inputs, or usage mode.
3. Open any capsule's HTML README or review page for the styled document view.
4. Jump into the matching challenge_* folder when you want to iterate on the code.

Quick Iteration Loop

When capsule code or review markdown changes, regenerate the local docs:

node build-embedded-docs.mjs
node build-static-doc-pages.mjs

Then reopen index.html locally or refresh the GitHub Pages site after pushing.

Notes

• The current cloned challenge set in this repo starts at Challenge 02.
• The review status labels are intentionally honest: some capsules are strong demonstrations and some remain incomplete, but none are currently blocked.
• The atlas and doc pages are static and can be opened directly in a browser over file://, with no local server required.