Skip to content

Commit 180fac9

Browse files
manuelcorpasclaude
manuelcorpas
and
claude
committed
docs: replace hackathon homepage with general docs hub, add Research tab with Genomebook
- Homepage now shows Get Started cards (Setup, First Skill, Build, Skills, Research, Deploy) - New Research section with Genomebook project page (NMI submission, demo, YouTube, reproducibility) - Research index includes publications table (Genomebook, HEIM, Bias Amplification Cascade) - Nav restructured: Skills promoted, Research tab added, Hackathon moved to archive position - Quick install section on homepage Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
1 parent a1c0789 commit 180fac9

4 files changed

Lines changed: 216 additions & 68 deletions

File tree

‎docs/index.md‎

Lines changed: 43 additions & 49 deletions
Original file line numberDiff line numberDiff line change
@@ -1,91 +1,85 @@
11
---
2-
title: ClawBio Hackathon — Agentic Genomics
3-
description: Build AI-powered bioinformatics skills at Imperial College London. 19 March 2026.
2+
title: ClawBio Documentation
3+
description: Technical documentation, tutorials, skill reference, and research projects for ClawBio, the bioinformatics-native AI agent skill library.
44
---
55

66
<div class="hero">
7-
<h1 class="hero__title">ClawBio Hackathon: Agentic Genomics</h1>
8-
<p class="hero__subtitle">19 March 2026 · Imperial College London · Build AI skills for bioinformatics</p>
7+
<h1 class="hero__title">ClawBio Documentation</h1>
8+
<p class="hero__subtitle">Technical docs, tutorials, and research for the bioinformatics AI skill library</p>
99
<p>
10-
<a href="https://luma.com/kolhdoi9" class="md-button md-button--primary">Register on Luma</a>
10+
<a href="https://clawbio.ai" class="md-button md-button--primary">ClawBio Home</a>
1111
&nbsp;
12-
<a href="hackathon/" class="md-button">Hackathon Guide</a>
12+
<a href="https://github.com/ClawBio/ClawBio" class="md-button">GitHub</a>
1313
</p>
1414
</div>
1515

16-
<h2 class="section-heading">Quick Path</h2>
16+
<h2 class="section-heading">Get Started</h2>
1717

1818
<div class="tutorial-cards">
1919

20-
<a class="tutorial-card" href="hackathon/">
20+
<a class="tutorial-card" href="tutorials/setup/">
2121
<div class="tutorial-card__header">
22-
<span class="difficulty-badge difficulty-badge--event">Event</span>
23-
<span class="time-estimate">5 min</span>
24-
</div>
25-
<h3 class="tutorial-card__title">Hackathon Guide</h3>
26-
<p class="tutorial-card__desc">Full timetable, tracks, judging criteria, and project ideas.</p>
27-
</a>
28-
29-
<a class="tutorial-card" href="hackathon/presentation/">
30-
<div class="tutorial-card__header">
31-
<span class="difficulty-badge difficulty-badge--event">Event</span>
22+
<span class="difficulty-badge difficulty-badge--beginner">Beginner</span>
3223
<span class="time-estimate">10 min</span>
3324
</div>
34-
<h3 class="tutorial-card__title">Presentation Slides</h3>
35-
<p class="tutorial-card__desc">Intro slides covering ClawBio, SKILL.md, and what to build today.</p>
25+
<h3 class="tutorial-card__title">Setup</h3>
26+
<p class="tutorial-card__desc">Clone ClawBio, install dependencies, and run your first demo skill.</p>
3627
</a>
3728

38-
<a class="tutorial-card" href="hackathon/agentic-tools/">
29+
<a class="tutorial-card" href="tutorials/run-your-first-skill/">
3930
<div class="tutorial-card__header">
40-
<span class="difficulty-badge difficulty-badge--tutorial">Tutorial</span>
31+
<span class="difficulty-badge difficulty-badge--beginner">Beginner</span>
4132
<span class="time-estimate">15 min</span>
4233
</div>
43-
<h3 class="tutorial-card__title">Agentic Tools Tutorial</h3>
44-
<p class="tutorial-card__desc">Use Claude Code and AI coding assistants to build skills faster.</p>
34+
<h3 class="tutorial-card__title">Run Your First Skill</h3>
35+
<p class="tutorial-card__desc">Run PharmGx, Equity Scorer, or NutriGx with demo data and explore the output.</p>
4536
</a>
4637

47-
<a class="tutorial-card" href="hackathon/setup/">
38+
<a class="tutorial-card" href="tutorials/build-a-skill/">
4839
<div class="tutorial-card__header">
49-
<span class="difficulty-badge difficulty-badge--beginner">Beginner</span>
50-
<span class="time-estimate">10 min</span>
51-
<span class="tutorial-card__step">STEP 1</span>
40+
<span class="difficulty-badge difficulty-badge--intermediate">Intermediate</span>
41+
<span class="time-estimate">30 min</span>
5242
</div>
53-
<h3 class="tutorial-card__title">Setup</h3>
54-
<p class="tutorial-card__desc">Clone ClawBio, install dependencies, and run your first demo skill.</p>
43+
<h3 class="tutorial-card__title">Build a Skill</h3>
44+
<p class="tutorial-card__desc">Write a SKILL.md, add Python implementation, and submit a PR.</p>
5545
</a>
5646

57-
<a class="tutorial-card" href="hackathon/first-skill/">
47+
<a class="tutorial-card" href="skills/">
5848
<div class="tutorial-card__header">
59-
<span class="difficulty-badge difficulty-badge--beginner">Beginner</span>
60-
<span class="time-estimate">20 min</span>
61-
<span class="tutorial-card__step">STEP 2</span>
49+
<span class="difficulty-badge difficulty-badge--tutorial">Reference</span>
6250
</div>
63-
<h3 class="tutorial-card__title">Your First Skill</h3>
64-
<p class="tutorial-card__desc">Write a SKILL.md from scratch and see it run end-to-end.</p>
51+
<h3 class="tutorial-card__title">Skill Library</h3>
52+
<p class="tutorial-card__desc">Browse all available skills: pharmacogenomics, GWAS, scRNA-seq, equity scoring, and more.</p>
6553
</a>
6654

67-
<a class="tutorial-card" href="hackathon/add-python/">
55+
<a class="tutorial-card" href="research/">
6856
<div class="tutorial-card__header">
69-
<span class="difficulty-badge difficulty-badge--intermediate">Intermediate</span>
70-
<span class="time-estimate">20 min</span>
71-
<span class="tutorial-card__step">STEP 3</span>
57+
<span class="difficulty-badge difficulty-badge--event">Research</span>
7258
</div>
73-
<h3 class="tutorial-card__title">Add Python</h3>
74-
<p class="tutorial-card__desc">Add a Python implementation to your skill with real bioinformatics logic.</p>
59+
<h3 class="tutorial-card__title">Research Projects</h3>
60+
<p class="tutorial-card__desc">Active research built on ClawBio: Genomebook, HEIM, and more.</p>
7561
</a>
7662

77-
<a class="tutorial-card" href="hackathon/submit/">
63+
<a class="tutorial-card" href="deployment/">
7864
<div class="tutorial-card__header">
79-
<span class="difficulty-badge difficulty-badge--beginner">Beginner</span>
80-
<span class="time-estimate">10 min</span>
81-
<span class="tutorial-card__step">STEP 4</span>
65+
<span class="difficulty-badge difficulty-badge--intermediate">Intermediate</span>
8266
</div>
83-
<h3 class="tutorial-card__title">Test & Submit</h3>
84-
<p class="tutorial-card__desc">Validate your skill, run tests, and submit your hackathon entry.</p>
67+
<h3 class="tutorial-card__title">Deployment</h3>
68+
<p class="tutorial-card__desc">Deploy ClawBio via Docker, Railway, or private cloud.</p>
8569
</a>
8670

8771
</div>
8872

8973
---
9074

91-
[Skill Library](skills/index.md) · [SKILL.md Spec](reference/skillmd-spec.md) · [Contributing](contributing/index.md) · [All Tutorials](tutorials/index.md)
75+
## Quick Install
76+
77+
```bash
78+
git clone https://github.com/ClawBio/ClawBio.git && cd ClawBio
79+
pip install -r requirements.txt
80+
python clawbio.py run pharmgx --demo
81+
```
82+
83+
---
84+
85+
[Skill Library](skills/index.md) · [SKILL.md Spec](reference/skillmd-spec.md) · [Contributing](contributing/index.md) · [All Tutorials](tutorials/index.md) · [Research](research/index.md)

‎docs/research/genomebook.md‎

Lines changed: 118 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,118 @@
1+
---
2+
title: "Genomebook: Mendelian Inheritance in LLM Agents"
3+
description: Simulating Mendelian inheritance of behavioural traits in large language model agents across 100 generations.
4+
---
5+
6+
# Genomebook
7+
8+
**Mendelian inheritance of behavioural traits in LLM agents**
9+
10+
Genomebook is a simulation framework that gives LLM agents a genome, lets them reproduce with Mendelian inheritance, and observes how genetic traits, disease burden, and social behaviour evolve across generations. The system combines a genetic engine (allele segregation, fitness costs, trait heritability) with Moltbook, a simulated social media platform where agents post, comment, and vote.
11+
12+
<div style="text-align: center; margin: 2em 0;">
13+
<a href="https://clawbio.ai/slides/genomebook/demo.html" class="md-button md-button--primary">Live Demo: Genomebook Observatory</a>
14+
&nbsp;
15+
<a href="https://github.com/ClawBio/ClawBio/tree/main/GENOMEBOOK" class="md-button">GitHub</a>
16+
</div>
17+
18+
---
19+
20+
## Video Series
21+
22+
A full walkthrough of Genomebook is available as a YouTube playlist covering the concept, implementation, results, and discussion.
23+
24+
<div style="text-align: center; margin: 2em 0;">
25+
<a href="https://www.youtube.com/watch?v=N5vGquaTqnM&list=PLRLOsiin0YSSkh3s743OHXL_paSJjuK_T">
26+
Watch the Genomebook video series on YouTube
27+
</a>
28+
</div>
29+
30+
---
31+
32+
## Key Findings
33+
34+
- **Directional genetic drift**: Fitness-linked alleles show consistent directional change across 100 generations, with trait means diverging from founder values
35+
- **Mendelian inheritance is necessary**: Ablation condition with no inheritance produces flat trait trajectories at ~0.5, confirming heredity drives observed dynamics
36+
- **Prompt conditioning shapes behaviour**: Agents with DNA.md in their system prompt produce significantly more genetics-related discourse and show higher topic inheritance rates
37+
- **Cross-model portability**: Results replicate qualitatively across GPT and Claude model families
38+
39+
## Experimental Design
40+
41+
The study uses 8 conditions across two tiers:
42+
43+
### Tier 1: Genetics-only (zero cost, 100 generations, 20 replications each)
44+
45+
| Condition | Purpose |
46+
|-----------|---------|
47+
| **Standard** | Full system: compatibility scoring + fitness costs + Mendelian inheritance |
48+
| **Random mating** | Does selective pairing matter? |
49+
| **Neutral fitness** | Does fitness pressure drive directional change? |
50+
| **No inheritance** | Is heredity itself necessary? |
51+
| **Prompt-only inheritance** | Can trait drift emerge without a genotype layer? |
52+
53+
### Tier 2: Behavioural (LLM-powered, replicated shorter runs)
54+
55+
| Condition | LLM | Replicates | Purpose |
56+
|-----------|-----|------------|---------|
57+
| **Standard + Moltbook** | GPT-5.4-mini | 3 | Primary behavioural data |
58+
| **No-DNA.md + Moltbook** | GPT-5.4-mini | 3 | Isolate prompt conditioning |
59+
| **Standard + Moltbook (Claude)** | Claude Haiku 4.5 | 2 | Cross-model portability |
60+
61+
## Figures
62+
63+
The manuscript includes 8 figures at 600 DPI:
64+
65+
1. **Graphical abstract**: pipeline diagram
66+
2. **Trait drift**: 9-panel trait trajectories (single run)
67+
3. **Allele frequency trajectories**: 8 loci across 100 generations
68+
4. **Disease prevalence heatmap**: 18 conditions
69+
5. **Vocabulary evolution**: topic inheritance patterns
70+
6. **PCA of genotypes**: 626 genotypes + population growth curve
71+
7. **Replicated traits**: 3 conditions, 20 runs, 95% CI
72+
8. **Replicated allele frequencies**: 2 conditions comparison
73+
74+
## Reproducibility
75+
76+
All experiments are fully reproducible:
77+
78+
```bash
79+
# Clone the repo
80+
git clone https://github.com/ClawBio/ClawBio.git && cd ClawBio/GENOMEBOOK
81+
82+
# Run all 80 Tier 1 simulations (4 conditions x 20 seeds)
83+
python data/run_experiments.py
84+
85+
# Regenerate all figures
86+
python figures/generate_figures.py
87+
python figures/generate_replication_figures.py
88+
```
89+
90+
| File | Purpose |
91+
|------|---------|
92+
| `data/run_experiments.py` | Runs all 80 simulations |
93+
| `data/experiment_results.json` | Full results from 80 simulations |
94+
| `figures/generate_figures.py` | Regenerates Figs 1-6 |
95+
| `figures/generate_replication_figures.py` | Regenerates Figs 7-8 |
96+
| `references/references.bib` | Master bibliography (25 citations) |
97+
98+
## Manuscript
99+
100+
**Status**: Under revision for Nature Machine Intelligence
101+
102+
| Format | Use |
103+
|--------|-----|
104+
| `final/genomebook_NMI.docx` | Primary submission file |
105+
| `final/genomebook_NMI.pdf` | For review/reference |
106+
| `final/genomebook_NMI.tex` | LaTeX source for revisions |
107+
| `final/references.bib` | BibTeX bibliography |
108+
109+
## Founders
110+
111+
The simulation starts with 50 historical figures as founders, each encoded with 26 trait scores using a fixed rubric (Low: 0.20-0.35, Moderate: 0.40-0.55, High: 0.60-0.75, Very high: 0.80-0.95). Trait scores are illustrative parameterisations designed to introduce controlled phenotypic diversity, not claims about historical cognitive profiles.
112+
113+
## Links
114+
115+
- [Live Demo: Genomebook Observatory](https://clawbio.ai/slides/genomebook/demo.html)
116+
- [YouTube series](https://www.youtube.com/watch?v=N5vGquaTqnM&list=PLRLOsiin0YSSkh3s743OHXL_paSJjuK_T)
117+
- [GitHub: GENOMEBOOK](https://github.com/ClawBio/ClawBio/tree/main/GENOMEBOOK)
118+
- [GitHub: Publications](https://github.com/ClawBio/ClawBio/tree/main/GENOMEBOOK)

‎docs/research/index.md‎

Lines changed: 33 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,33 @@
1+
---
2+
title: Research Projects
3+
description: Active research projects built on ClawBio infrastructure and skills.
4+
---
5+
6+
# Research Projects
7+
8+
ClawBio is not just a skill library. It is the foundation for active research in computational genomics, health equity, and AI-driven biology. This section documents ongoing projects, their methods, data, and outputs.
9+
10+
## Active Projects
11+
12+
<div class="tutorial-cards">
13+
14+
<a class="tutorial-card" href="genomebook/">
15+
<div class="tutorial-card__header">
16+
<span class="difficulty-badge difficulty-badge--event">Active</span>
17+
<span class="time-estimate">NMI submission</span>
18+
</div>
19+
<h3 class="tutorial-card__title">Genomebook</h3>
20+
<p class="tutorial-card__desc">Mendelian inheritance of behavioural traits in LLM agents. Simulated evolution across 100 generations with genetic drift, fitness selection, and social media behaviour.</p>
21+
</a>
22+
23+
</div>
24+
25+
---
26+
27+
## Publications
28+
29+
| Project | Status | Venue | Links |
30+
|---------|--------|-------|-------|
31+
| **Genomebook** | Under revision | Nature Machine Intelligence | [Paper](genomebook/) · [Demo](https://clawbio.ai/slides/genomebook/demo.html) · [GitHub](https://github.com/ClawBio/ClawBio/tree/main/GENOMEBOOK) |
32+
| **HEIM** | Under review | Nature Health | [Preprint](https://doi.org/10.1101/2024.11.25.24317897) · [Skill](../skills/equity-scorer/) |
33+
| **Bias Amplification Cascade** | Under revision | Communications Biology | [GitHub](https://github.com/manuelcorpas/bias-amplification-cascade) |

‎mkdocs.yml‎

Lines changed: 22 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
site_name: ClawBio Documentation
22
site_url: https://docs.clawbio.ai
3-
site_description: The reference repository for biological AI agent skills. Curated. Reproducible. Open.
3+
site_description: Technical documentation, tutorials, and research for ClawBio, the bioinformatics-native AI agent skill library.
44
site_author: Manuel Corpas
55
repo_url: https://github.com/ClawBio/ClawBio
66
repo_name: ClawBio/ClawBio
@@ -35,13 +35,17 @@ theme:
3535

3636
nav:
3737
- Home: index.md
38-
- Hackathon:
39-
- Guide: hackathon/index.md
40-
- Setup: hackathon/setup.md
41-
- Build a Skill: hackathon/first-skill.md
42-
- Add Python: hackathon/add-python.md
43-
- Submit: hackathon/submit.md
44-
- Agentic Tools: hackathon/agentic-tools.md
38+
- Skills:
39+
- Skill Library: skills/index.md
40+
- PharmGx Reporter: skills/pharmgx-reporter.md
41+
- scRNA Orchestrator: skills/scrna-orchestrator.md
42+
- Equity Scorer (HEIM): skills/equity-scorer.md
43+
- NutriGx Advisor: skills/nutrigx-advisor.md
44+
- Genome Compare: skills/genome-compare.md
45+
- GWAS PRS: skills/gwas-prs.md
46+
- GWAS Lookup: skills/gwas-lookup.md
47+
- Galaxy Bridge: skills/galaxy-bridge.md
48+
- RNA-seq DE: skills/rnaseq-de.md
4549
- Tutorials:
4650
- Overview: tutorials/index.md
4751
- Basics:
@@ -60,27 +64,26 @@ nav:
6064
- Run Your First Skill: tutorials/run-your-first-skill.md
6165
- Build a Skill: tutorials/build-a-skill.md
6266
- Telegram Bot: tutorials/telegram-bot.md
67+
- Research:
68+
- Overview: research/index.md
69+
- Genomebook: research/genomebook.md
6370
- Deployment:
6471
- Overview: deployment/index.md
6572
- Docker: deployment/docker.md
6673
- Railway: deployment/railway.md
6774
- Private Cloud: deployment/private-cloud.md
68-
- Skills:
69-
- Skill Library: skills/index.md
70-
- PharmGx Reporter: skills/pharmgx-reporter.md
71-
- scRNA Orchestrator: skills/scrna-orchestrator.md
72-
- Equity Scorer (HEIM): skills/equity-scorer.md
73-
- NutriGx Advisor: skills/nutrigx-advisor.md
74-
- Genome Compare: skills/genome-compare.md
75-
- GWAS PRS: skills/gwas-prs.md
76-
- GWAS Lookup: skills/gwas-lookup.md
77-
- Galaxy Bridge: skills/galaxy-bridge.md
78-
- RNA-seq DE: skills/rnaseq-de.md
7975
- Reference:
8076
- SKILL.md Spec: reference/skillmd-spec.md
8177
- CLI: reference/cli.md
8278
- Security: reference/security.md
8379
- Contributing: contributing/index.md
80+
- Hackathon:
81+
- Guide: hackathon/index.md
82+
- Setup: hackathon/setup.md
83+
- Build a Skill: hackathon/first-skill.md
84+
- Add Python: hackathon/add-python.md
85+
- Submit: hackathon/submit.md
86+
- Agentic Tools: hackathon/agentic-tools.md
8487

8588
plugins:
8689
- search

0 commit comments

Comments
 (0)