Start

# Bio-Research Start

> If you see unfamiliar placeholders or need to check which tools are connected, see [CONNECTORS.md](../../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.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/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:

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.