Skip to content

Commit f44fc43

Browse files
drorhilmandrorhilman
committed
readme
1 parent 824a7c5 commit f44fc43

2 files changed

Lines changed: 87 additions & 1 deletion

File tree

‎README.md‎

Lines changed: 86 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,86 @@
1+
# Allen Institute Nautilex 2026 Challenge Capsules
2+
3+
This repository documents an AI-driven implementation sprint for the **Allen Institute Nautilex 2026** hackathon challenges.
4+
5+
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.
6+
7+
Over **4 days** and **3 implementation / review iterations**, the work was driven through **Code Ocean Aqua** and **Claude Code**:
8+
9+
- **Aqua** was used as the Code Ocean agent layer for building and running the capsules.
10+
- **Claude Code** was used as the coding agent to implement and revise the capsules.
11+
- Claude Code was also used as a critic across iterations to review outputs, identify gaps, and drive the next round of fixes.
12+
13+
## Live Atlas
14+
15+
- **GitHub Pages atlas:** https://codeocean.github.io/challenges-capsules/
16+
- **Repo atlas source:** [index.html](./index.html)
17+
- **Repo capsule index:** [index.md](./index.md)
18+
- **Iteration 03 summary:** [working-capsules-summary.md](./review-challanges-iteration-03/working-capsules-summary.md)
19+
20+
## Outcome
21+
22+
The current repo snapshot covers **15 capsules** for **Challenges 02-16**.
23+
24+
- **10 completed**
25+
- **4 partially completed**
26+
- **1 blocked**
27+
28+
The most important outcome is not just the code. It is the combination of:
29+
30+
- runnable capsule implementations
31+
- capsule-specific READMEs
32+
- review summaries with honest limitations
33+
- a local and hosted HTML atlas for fast navigation
34+
35+
## What Is In This Repo
36+
37+
- `challenge_02_*` to `challenge_16_*`: the capsule codebases
38+
- [`index.html`](./index.html): the main navigable atlas
39+
- [`docs/`](./docs): styled HTML pages for every local README and review summary
40+
- [`review-challanges-iteration-03/`](./review-challanges-iteration-03): iteration-03 review bundle
41+
- [`build-embedded-docs.mjs`](./build-embedded-docs.mjs): rebuilds the embedded markdown bundle
42+
- [`build-static-doc-pages.mjs`](./build-static-doc-pages.mjs): regenerates the static HTML doc pages
43+
44+
## Quick Navigation
45+
46+
| Challenge | Capsule | Status | Live README | Live Review |
47+
|---|---|---:|---|---|
48+
| 02 | Agentic Data Harmonization | Completed | [README](https://codeocean.github.io/challenges-capsules/docs/challenge-02-readme.html) | [Review](https://codeocean.github.io/challenges-capsules/docs/challenge-02-review.html) |
49+
| 03 | Enhancer Designer | Completed | [README](https://codeocean.github.io/challenges-capsules/docs/challenge-03-readme.html) | [Review](https://codeocean.github.io/challenges-capsules/docs/challenge-03-review.html) |
50+
| 04 | Light Sheet Alignment QC | Completed | [README](https://codeocean.github.io/challenges-capsules/docs/challenge-04-readme.html) | [Review](https://codeocean.github.io/challenges-capsules/docs/challenge-04-review.html) |
51+
| 05 | Automate Your Productivity | Partial | [README](https://codeocean.github.io/challenges-capsules/docs/challenge-05-readme.html) | [Review](https://codeocean.github.io/challenges-capsules/docs/challenge-05-review.html) |
52+
| 06 | Plasmid Forge | Partial | [README](https://codeocean.github.io/challenges-capsules/docs/challenge-06-readme.html) | [Review](https://codeocean.github.io/challenges-capsules/docs/challenge-06-review.html) |
53+
| 07 | Engineering Automation | Completed | [README](https://codeocean.github.io/challenges-capsules/docs/challenge-07-readme.html) | [Review](https://codeocean.github.io/challenges-capsules/docs/challenge-07-review.html) |
54+
| 08 | Query BFF | Completed | [README](https://codeocean.github.io/challenges-capsules/docs/challenge-08-readme.html) | [Review](https://codeocean.github.io/challenges-capsules/docs/challenge-08-review.html) |
55+
| 09 | BindCrafting | Partial | [README](https://codeocean.github.io/challenges-capsules/docs/challenge-09-readme.html) | [Review](https://codeocean.github.io/challenges-capsules/docs/challenge-09-review.html) |
56+
| 10 | NeuroBase Foundation Model Evaluation | Blocked | [README](https://codeocean.github.io/challenges-capsules/docs/challenge-10-readme.html) | [Review](https://codeocean.github.io/challenges-capsules/docs/challenge-10-review.html) |
57+
| 11 | ABC Atlas Literature Assistant | Completed | [README](https://codeocean.github.io/challenges-capsules/docs/challenge-11-readme.html) | [Review](https://codeocean.github.io/challenges-capsules/docs/challenge-11-review.html) |
58+
| 12 | Brain Map + BKP Assistant | Completed | [README](https://codeocean.github.io/challenges-capsules/docs/challenge-12-readme.html) | [Review](https://codeocean.github.io/challenges-capsules/docs/challenge-12-review.html) |
59+
| 13 | Croissant Pipeline | Completed | [README](https://codeocean.github.io/challenges-capsules/docs/challenge-13-readme.html) | [Review](https://codeocean.github.io/challenges-capsules/docs/challenge-13-review.html) |
60+
| 14 | Segment Intestine Villi | Completed | [README](https://codeocean.github.io/challenges-capsules/docs/challenge-14-readme.html) | [Review](https://codeocean.github.io/challenges-capsules/docs/challenge-14-review.html) |
61+
| 15 | Allen Single Cell Model Pantry | Partial | [README](https://codeocean.github.io/challenges-capsules/docs/challenge-15-readme.html) | [Review](https://codeocean.github.io/challenges-capsules/docs/challenge-15-review.html) |
62+
| 16 | SciDEX | Completed | [README](https://codeocean.github.io/challenges-capsules/docs/challenge-16-readme.html) | [Review](https://codeocean.github.io/challenges-capsules/docs/challenge-16-review.html) |
63+
64+
## Fastest Way To Explore
65+
66+
1. Open the live atlas: https://codeocean.github.io/challenges-capsules/
67+
2. Use the sortable top table to scan by challenge, status, inputs, or usage mode.
68+
3. Open any capsule's HTML README or review page for the styled document view.
69+
4. Jump into the matching `challenge_*` folder when you want to iterate on the code.
70+
71+
## Quick Iteration Loop
72+
73+
When capsule code or review markdown changes, regenerate the local docs:
74+
75+
```bash
76+
node build-embedded-docs.mjs
77+
node build-static-doc-pages.mjs
78+
```
79+
80+
Then reopen [`index.html`](./index.html) locally or refresh the GitHub Pages site after pushing.
81+
82+
## Notes
83+
84+
- The current cloned challenge set in this repo starts at **Challenge 02**.
85+
- The review status labels are intentionally honest: some capsules are strong demonstrations, some are incomplete, and one remains blocked.
86+
- The atlas and doc pages are static and can be opened directly in a browser over `file://`, with no local server required.

‎index.html‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -29,7 +29,7 @@
2929
<p class="brand-note">A local, navigable guide to the Allen challenge capsules.</p>
3030
</div>
3131
</div>
32-
<h1>Allen challenge capsules, explained as runnable Code Ocean products.</h1>
32+
<h1>Allen Institute Nautilex 2026 challenges, solved by Code Ocean Aqua as Code Ocean capsules.</h1>
3333
<p class="hero-intro">
3434
Explore how each capsule frames a research problem, how the codebase solves
3535
it, what to attach in Code Ocean, and what outputs to expect. The table is

0 commit comments

Comments
 (0)