ClawBio

🦖 ClawBio Architecture

Overview

ClawBio is a collection of modular AI agent skills for bioinformatics, designed around three principles: local-first execution, reproducible analysis, and composable workflows.

System Design

                    ┌─────────────────────┐
                    │    User Request      │
                    │  (natural language)  │
                    └──────────┬──────────┘
                               │
                    ┌──────────▼──────────┐
                    │   Bio Orchestrator   │
                    │  (routing + planning │
                    │   + report assembly) │
                    └──────────┬──────────┘
                               │
              ┌────────────────┼────────────────┐
              │                │                 │
    ┌─────────▼───────┐ ┌─────▼──────┐ ┌───────▼────────┐
    │  Equity Scorer   │ │ Seq Wrangler│ │ Struct Predictor│
    │  VCF Annotator   │ │ scRNA Orch  │ │ Lit Synthesizer │
    │                  │ │             │ │ Repro Enforcer  │
    └─────────┬───────┘ └─────┬──────┘ └───────┬────────┘
              │                │                 │
              └────────────────┼────────────────┘
                               │
                    ┌──────────▼──────────┐
                    │   Output Layer       │
                    │  - Markdown report   │
                    │  - Figures (PNG/SVG) │
                    │  - Audit log         │
                    │  - Repro bundle      │
                    └─────────────────────┘

Routing Logic

The Bio Orchestrator routes requests based on:

1. File extension: .vcf -> equity-scorer/vcf-annotator, .fastq -> seq-wrangler, etc.
2. Keyword matching: “diversity” -> equity-scorer, “structure” -> struct-predictor, etc.
3. User intent: Explicit skill names override automatic routing.
4. Chaining: Multi-step requests trigger sequential skill invocation with output piping.

Skill Independence

Every skill works standalone. The Bio Orchestrator adds:

• Automatic routing (user does not need to know skill names)
• Multi-skill chaining (pipe output of one skill to the next)
• Unified reporting (combine results from multiple skills)
• Reproducibility wrapping (Repro Enforcer applied automatically)

A user can invoke any skill directly without the orchestrator.

Data Flow

Input File(s)
    │
    ▼
Validation (file type, format, size checks)
    │
    ▼
Processing (skill-specific computation)
    │
    ▼
Results (tables, metrics, intermediate files)
    │
    ▼
Visualisation (matplotlib/seaborn figures)
    │
    ▼
Report Assembly (markdown + embedded figures)
    │
    ▼
Reproducibility Export (conda env, commands, checksums)
    │
    ▼
Audit Log Append (timestamped action record)

Privacy Model

ClawBio enforces a strict local-first privacy model:

• No network calls for data processing. All computation happens locally.
• Optional network only for: literature search (PubMed API), structure database queries (PDB/UniProt), and package installation.
• Explicit consent required before any data leaves the machine.
• File access scoping: Skills operate within the current working directory by default. Access to parent directories requires user confirmation.

Reproducibility Contract

Every analysis produces:

1. commands.sh: Exact shell commands to reproduce the analysis without the agent.
2. environment.yml: Conda environment specification with pinned versions.
3. checksums.sha256: SHA-256 hashes of all input files.
4. analysis_log.md: Timestamped record of every action taken.

This means any result can be reproduced on any machine with the same inputs, independent of OpenClaw.

Skill Packaging

Each skill is a directory containing:

skill-name/
├── SKILL.md          # Required: YAML frontmatter + markdown instructions
├── skill_name.py     # Optional: Python implementation
├── utils.py          # Optional: shared utilities
├── tests/            # Optional: test cases
│   └── test_skill.py
└── examples/         # Optional: example inputs/outputs
    ├── input.vcf
    └── expected_output.md

The SKILL.md is the primary artifact. The Python files are supporting code that the agent invokes via shell commands. This separation means:

• Skills can be reviewed as markdown (human-readable)
• Python code can be tested independently
• Skills work with any compatible agent platform, not just OpenClaw

Integration with OpenBio

The existing OpenBio skill provides API access to:

• PDB (protein structures)
• UniProt (protein sequences and annotations)
• ChEMBL (bioactivity data)
• Pathway databases

ClawBio skills can call OpenBio for database lookups while keeping all computation local. For example, Struct Predictor might use OpenBio to fetch a reference structure from PDB, then run local AlphaFold for comparison.

Extensibility

New skills follow the template at templates/SKILL-TEMPLATE.md. The Bio Orchestrator routing table is designed to be extended: add a new entry mapping file types or keywords to your skill, and the orchestrator routes to it automatically.

Community submissions go through ClawHub or direct PR to this repository. 🦖

This site is open source. Improve this page.