Claude Science: Prompts, Skills, and MCP

System prompts, scientific skills, and Bio Research MCP configuration.

Open directly

Category	Files
General prompts	Opus 5, Fable 5
Claude Science prompts	Opus 5, Fable 5
Research workflow	Conducting scientific research
Bio Research setup	Start skill, MCP configuration, connector map

Architecture

prompts/
├── general/                         General Opus 5 and Fable 5 prompts
│   └── fragments/                   Compaction, commands, reminders, and tools
└── claude-science/                  Complete Claude Science prompts
    └── fragments/                   Claude Science prompt components

skills/
├── conducting-scientific-research/  General scientific workflow
├── bio-research-start/              Bio Research orientation skill
├── clinical-trial-protocol/         Clinical protocol workflow
├── instrument-data-to-allotrope/    Instrument-data conversion
├── nextflow-development/            nf-core pipeline workflows
├── scientific-problem-selection/    Research strategy workflow
├── scvi-tools/                      Single-cell omics analysis
└── single-cell-rna-qc/              Single-cell RNA quality control

mcp/
└── bio-research/
    ├── .mcp.json                    11 Bio Research MCP definitions
    ├── CONNECTORS.md                Tool categories and configured servers
    └── .claude-plugin/plugin.json   Plugin metadata

Conventions

• Open complete prompts directly from prompts/general/ or prompts/claude-science/.
• fragments/ only contains components used to compose prompts. It never contains skills.
• Every skill is directly under skills/<skill-name>/; begin with its SKILL.md.
• MCP configuration lives under mcp/. It contains server definitions and connector documentation, not skill instructions.

Claude Science overview

Claude Science is framed as a research workbench with persistent Python/R kernels, managed tool permissions, durable artifacts, and optional specialist-agent work.

flowchart LR
    U[Researcher] --> H[Claude Science harness]
    H --> M[Claude model]
    M --> T[Managed tools]
    T --> K[Python / R kernels]
    T --> A[Artifacts and provenance]
    T --> S[Specialist agents]
    M --> U

License

Repository material is licensed under LICENSE.

Material under skills/ and mcp/ is separately licensed under Apache-2.0. See third-party licenses.