Start
It checks the connection status of various MCP servers and lists the analysis skills available within the plugin.
Install
npx promptshop add startDetails
What This Skill Does
This skill serves as an onboarding guide for the Bio-Research plugin, helping users understand its capabilities and available tools. It checks the connection status of various MCP servers and lists the analysis skills available within the plugin. It is designed to orient new users and provide a starting point for their research.
When to Use
- Introduce new users to the Bio-Research plugin.
- Check the connection status of MCP servers.
- List available literature and data sources.
- Survey available analysis skills within the plugin.
- Help users understand the plugin's capabilities.
- Provide a starting point for research tasks.
Key Features
Displays a welcome message introducing the plugin. Checks the connection status of MCP servers. Groups available tools by category (Literature, Drug Discovery, etc.). Lists available analysis skills with descriptions. Provides a table summarizing the capabilities of each skill. Guides users through the initial steps of using the plugin.
Manual Installation
Manual installation## 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 Clinical Trials.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 sc RNA-seq data with MAD-based filtering |
| scvi-tools | Deep learning for single-cell omics (sc VI, sc ANVI, total VI, Peak VI, 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.mcpb from https://github.com/10XGenomics/txg-mcp/releases ~~tool database (Harvard MIMS) — AI tools for scientific discovery Install: Download tooluniverse.mcpb from https://github.com/mims-harvard/Tool Universe/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. 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.
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 Clinical Trials.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.
List the analysis skills available in this plugin:
| Skill | What It Does |
|---|---|
| Single-Cell RNA QC | Quality control for sc RNA-seq data with MAD-based filtering |
| scvi-tools | Deep learning for single-cell omics (sc VI, sc ANVI, total VI, Peak VI, 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:
~~genomics platform — Access cloud analysis data and workflows Install: Download txg-node.mcpb from https://github.com/10XGenomics/txg-mcp/releases ~~tool database (Harvard MIMS) — AI tools for scientific discovery Install: Download tooluniverse.mcpb from https://github.com/mims-harvard/Tool Universe/releases
These require downloading binary files and are optional.
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.