How do I install the Start skill?

Run npx skillmds@latest add nota-america/start-2 in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Start safe to use?

This skill has not completed SkillMD's automated safety review yet. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Start?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Start free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

nota-america (@nota-america) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Start by nota-america — Agent Skill

Name: Start
Author: nota-america

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.

nota-america Updated Sep 17, 2026

File contents

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.

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:

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.

---name: start-2description: 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.---# 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: WelcomeDisplay this welcome message:```Bio-Research PluginYour 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 ServersTest 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 SkillsList 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 ServersMention 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/releasesThese require downloading binary files and are optional.## Step 5: Ask How to HelpAsk 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.

Frequently asked questions