Start
Set up your bio-research environment and explore available tools.
by anthropics · Apache-2.0
The skill
Set up your bio-research environment and explore available tools. Use when first getting oriented with the plugin, checking which literature, drug-discovery, or visualization MCP servers are connected, or surveying available analysis skills before starting a new project.
Bio-Research Start
If you see unfamiliar placeholders or need to check which tools are connected, see CONNECTORS.md.
You are helping a biological researcher get oriented with the bio-research plugin. Walk through the following steps in order.
Step 1: Welcome
Display this welcome message:
Bio-Research Plugin
Your AI-powered research assistant for the life sciences. This plugin brings
together literature search, data analysis pipelines,
and scientific strategy — all in one place.
Step 2: Check Available MCP Servers
Test which MCP servers are connected by listing available tools. Group the results:
Literature & Data Sources:
- ~~literature database — biomedical literature search
- ~~literature database — preprint access (biology and medicine)
- ~~journal access — academic publications
- ~~data repository — collaborative research data (Sage Bionetworks)
Drug Discovery & Clinical:
- ~~chemical database — bioactive compound database
- ~~drug target database — drug target discovery platform
- ClinicalTrials.gov — clinical trial registry
- ~~clinical data platform — clinical trial site ranking and platform help
Visualization & AI:
- ~~scientific illustration — create scientific figures and diagrams
- ~~AI research platform — AI for biology (histopathology, drug discovery)
Report which servers are connected and which are not yet set up.
Step 3: Survey Available Skills
List the analysis skills available in this plugin:
| Skill | What It Does |
|---|---|
| Single-Cell RNA QC | Quality control for scRNA-seq data with MAD-based filtering |
| scvi-tools | Deep learning for single-cell omics (scVI, scANVI, totalVI, PeakVI, etc.) |
| Nextflow Pipelines | Run nf-core pipelines (RNA-seq, WGS/WES, ATAC-seq) |
| Instrument Data Converter | Convert lab instrument output to Allotrope ASM format |
| Scientific Problem Selection | Systematic framework for choosing research problems |
Step 4: Optional Setup — Binary MCP Servers
Mention that two additional MCP servers are available as separate installations:
- ~~genomics platform — Access cloud analysis data and workflows
Install: Download
txg-node.mcpbfrom https://github.com/10XGenomics/txg-mcp/releases - ~~tool database (Harvard MIMS) — AI tools for scientific discovery
Install: Download
tooluniverse.mcpbfrom https://github.com/mims-harvard/ToolUniverse/releases
These require downloading binary files and are optional.
Step 5: Ask How to Help
Ask the researcher what they're working on today. Suggest starting points based on common workflows:
- Literature review — "Search ~~literature database for recent papers on [topic]"
- Analyze sequencing data — "Run QC on my single-cell data" or "Set up an RNA-seq pipeline"
- Drug discovery — "Search ~~chemical database for compounds targeting [protein]" or "Find drug targets for [disease]"
- Data standardization — "Convert my instrument data to Allotrope format"
- Research strategy — "Help me evaluate a new project idea"
Wait for the user's response and guide them to the appropriate tools and skills.
Use this skill
Connect your agent to the Skill Store MCP server and ask for it by ref: anthropics/start-93355051098.
Details
- Publisher
- anthropics
- Category
- Health & Life Sciences › Bioinformatics & genomics
- License
- Apache-2.0
- Updated
- 2026-10-15
References
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