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by anthropicsae1513ea94dcNo license27K starsListed Oct 8, 2026Updated Oct 8, 2026Repository updated today

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.

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AI-generated overview

Orients a biological researcher to a bio-research plugin by checking connected MCP servers and listing available analysis skills.

What it does
Walks a researcher through an onboarding sequence: it shows a welcome message, tests which MCP servers are connected by listing available tools, and groups them into literature and data sources, drug discovery and clinical, and visualization and AI. It then surveys the plugin's analysis skills in a table and points to two optional binary MCP server installations. Finally it asks what the researcher is working on and suggests starting points such as literature review, sequencing analysis, drug discovery, data standardization, or research strategy.
When to use it
Use when first getting oriented with the bio-research plugin, when checking which literature, drug-discovery, or visualization MCP servers are connected, or when surveying available analysis skills before starting a new project.
Requirements
Instructions only; no scripts are shipped. It relies on the agent's ability to list available MCP tools and on the plugin's connected MCP servers. Two optional MCP servers require downloading binary files from external release pages.

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 bringstogether 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:

SkillWhat It Does
Single-Cell RNA QCQuality control for scRNA-seq data with MAD-based filtering
scvi-toolsDeep learning for single-cell omics (scVI, scANVI, totalVI, PeakVI, etc.)
Nextflow PipelinesRun nf-core pipelines (RNA-seq, WGS/WES, ATAC-seq)
Instrument Data ConverterConvert lab instrument output to Allotrope ASM format
Scientific Problem SelectionSystematic framework for choosing research problems

Step 4: Optional Setup — Binary MCP Servers

Mention that two additional MCP servers are available as separate installations:

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:

  1. Literature review — "Search ~~literature database for recent papers on [topic]"
  2. Analyze sequencing data — "Run QC on my single-cell data" or "Set up an RNA-seq pipeline"
  3. Drug discovery — "Search ~~chemical database for compounds targeting [protein]" or "Find drug targets for [disease]"
  4. Data standardization — "Convert my instrument data to Allotrope format"
  5. Research strategy — "Help me evaluate a new project idea"

Wait for the user's response and guide them to the appropriate tools and skills.

Source and attribution

Source:anthropics/knowledge-work-pluginsinbio-research/skills/startat commitae1513e

License: No license

Content belongs to its original authors. SourceWeft indexes it from a public repository.

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