Get oriented with a biological research plugin by checking connected research tools and reviewing available analysis skills. Receive a connection summary, optional setup guidance, and suggested starting points for literature searches, sequencing analysis, drug discovery, or research planning.
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.
Review the instructions the agent will receive before you install.
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.
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.
Test which MCP servers are connected by listing available tools. Group the results:
Literature & Data Sources:
Drug Discovery & Clinical:
Visualization & AI:
Report which servers are connected and which are not yet set up.
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 |
Mention that two additional MCP servers are available as separate installations:
txg-node.mcpb from https://github.com/10XGenomics/txg-mcp/releasestooluniverse.mcpb from https://github.com/mims-harvard/ToolUniverse/releasesThese require downloading binary files and are optional.
Ask the researcher what they're working on today. Suggest starting points based on common workflows:
Wait for the user's response and guide them to the appropriate tools and skills.
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Review a design or web page against WCAG 2.1 AA, an accessibility standard. Organize findings on contrast, keyboard access, forms, and screen reader behavior, with severity levels and practical recommendations for fixes.
Build a single brief on an existing customer using available sales records, emails, documents, call notes, and internal chat. Understand the current situation, key contacts, recent discussions, and gaps that may need attention.
Build or refresh a strategic customer account plan from sales records, emails, and meeting transcripts. Organize goals, stakeholders, growth opportunities, risks, and dated actions into a document, then sync approved highlights to the customer relationship management system.
Research prospective companies and contacts, check existing customer records, and assess fit against your ideal customer profile. Receive a sourced brief covering recent developments, likely priorities, outreach talking points, and a suggested next step.
Research sales accounts using Common Room data to summarize company details, buying signals, ownership, and key contacts. Answer specific questions directly or prepare a broader briefing with evidence-based next steps, clearly identifying missing information.
Score and group accounts by customer fit and engagement, such as recent contact and open sales opportunities. Identify where to focus sales effort, choose next actions, and spot promising accounts with neglected outreach or missing information.