Start

1---2name: start3description: 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.4---5 6# Bio-Research Start7 8> If you see unfamiliar placeholders or need to check which tools are connected, see [CONNECTORS.md](../../CONNECTORS.md).9 10You are helping a biological researcher get oriented with the bio-research plugin. Walk through the following steps in order.11 12## Step 1: Welcome13 14Display this welcome message:15 16```17Bio-Research Plugin18 19Your AI-powered research assistant for the life sciences. This plugin brings20together literature search, data analysis pipelines,21and scientific strategy — all in one place.22```23 24## Step 2: Check Available MCP Servers25 26Test which MCP servers are connected by listing available tools. Group the results:27 28**Literature & Data Sources:**29- ~~literature database — biomedical literature search30- ~~literature database — preprint access (biology and medicine)31- ~~journal access — academic publications32- ~~data repository — collaborative research data (Sage Bionetworks)33 34**Drug Discovery & Clinical:**35- ~~chemical database — bioactive compound database36- ~~drug target database — drug target discovery platform37- ClinicalTrials.gov — clinical trial registry38- ~~clinical data platform — clinical trial site ranking and platform help39 40**Visualization & AI:**41- ~~scientific illustration — create scientific figures and diagrams42- ~~AI research platform — AI for biology (histopathology, drug discovery)43 44Report which servers are connected and which are not yet set up.45 46## Step 3: Survey Available Skills47 48List the analysis skills available in this plugin:49 50| Skill | What It Does |51|-------|-------------|52| **Single-Cell RNA QC** | Quality control for scRNA-seq data with MAD-based filtering |53| **scvi-tools** | Deep learning for single-cell omics (scVI, scANVI, totalVI, PeakVI, etc.) |54| **Nextflow Pipelines** | Run nf-core pipelines (RNA-seq, WGS/WES, ATAC-seq) |55| **Instrument Data Converter** | Convert lab instrument output to Allotrope ASM format |56| **Scientific Problem Selection** | Systematic framework for choosing research problems |57 58## Step 4: Optional Setup — Binary MCP Servers59 60Mention that two additional MCP servers are available as separate installations:61 62- **~~genomics platform** — Access cloud analysis data and workflows63  Install: Download `txg-node.mcpb` from https://github.com/10XGenomics/txg-mcp/releases64- **~~tool database** (Harvard MIMS) — AI tools for scientific discovery65  Install: Download `tooluniverse.mcpb` from https://github.com/mims-harvard/ToolUniverse/releases66 67These require downloading binary files and are optional.68 69## Step 5: Ask How to Help70 71Ask the researcher what they're working on today. Suggest starting points based on common workflows:72 731. **Literature review** — "Search ~~literature database for recent papers on [topic]"742. **Analyze sequencing data** — "Run QC on my single-cell data" or "Set up an RNA-seq pipeline"753. **Drug discovery** — "Search ~~chemical database for compounds targeting [protein]" or "Find drug targets for [disease]"764. **Data standardization** — "Convert my instrument data to Allotrope format"775. **Research strategy** — "Help me evaluate a new project idea"78 79Wait for the user's response and guide them to the appropriate tools and skills.