start
The facts
Its description
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.
The description the agent reads to decide when to use it.
When it starts
The agent picks this skill when a researcher is new to the bio-research plugin and wants to get oriented: seeing which literature, drug-discovery, or visualization MCP servers are connected, surveying the analysis skills the plugin offers, and being pointed toward a starting workflow. It is a first-run walkthrough rather than a task skill, so it fires on setup/orientation talk about the plugin itself.
Things a person might say (the model's guesses)
- “I just installed the bio-research plugin — where do I start?”
- “Which research tools and servers are connected for me right now?”
- “What can this bio-research plugin actually do?”
A model's summary of when it is used.
Stops for a person
1 line stops to ask a person
Lines that stop and wait for a person before going on. Found by matching words, so treat them as pointers.
What it leads to
- hands off to instrument-data-to-allotrope when the researcher wants instrument data standardized line 76
- hands off to nextflow-development when the researcher wants to set up a sequencing pipeline line 74
- hands off to scientific-problem-selection when the researcher wants help judging a project idea line 77
- hands off to single-cell-rna-qc when the researcher wants QC on single-cell data line 74
Other skills this one hands off to, calls, requires or offers instead, as a model read them.
Licence
Apache-2.0, from bio-research/LICENSE
The terms its author shares it under, which let it be shown here.
The text
Most marks come from matching words in the file, so treat them as pointers.
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.
Raw lines 1 to 11Step 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.
Raw lines 24 to 45Step 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.
Raw lines 58 to 68Step 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.
Raw lines 69 to 79From anthropics/knowledge-work-plugins at 2574e29, 2026-10-27. Skills read by DeepSeek V4.1 Flash on 2026-11-04. Summary and techniques by Claude Opus 5.5 on 2026-11-06.