start
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.
Best use case
start is best used when you need a repeatable AI agent workflow instead of a one-off prompt.
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.
Teams using start should expect a more consistent output, faster repeated execution, less prompt rewriting.
When to use this skill
- You want a reusable workflow that can be run more than once with consistent structure.
When not to use this skill
- You only need a quick one-off answer and do not need a reusable workflow.
- You cannot install or maintain the underlying files, dependencies, or repository context.
Installation
Claude Code / Cursor / Codex
Manual Installation
- Download SKILL.md from GitHub
- Place it in
.claude/skills/start/SKILL.mdinside your project - Restart your AI agent — it will auto-discover the skill
How start Compares
| Feature / Agent | start | Standard Approach |
|---|---|---|
| Platform Support | Not specified | Limited / Varies |
| Context Awareness | High | Baseline |
| Installation Complexity | Unknown | N/A |
Frequently Asked Questions
What does this skill do?
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.
Where can I find the source code?
You can find the source code on GitHub using the link provided at the top of the page.
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SKILL.md Source
# 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.
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