{
  "schema": "https://ai-atoms.com/schemas/skill-v1.json",
  "type": "skill",
  "id": "skill/start",
  "version": "1.0.0",
  "name": "start",
  "description": "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.",
  "system_prompt_fragment": "# Bio-Research Start\n\n> If you see unfamiliar placeholders or need to check which tools are connected, see [CONNECTORS.md](../../CONNECTORS.md).\n\nYou are helping a biological researcher get oriented with the bio-research plugin. Walk through the following steps in order.\n\n## Step 1: Welcome\n\nDisplay this welcome message:\n\n```\nBio-Research Plugin\n\nYour AI-powered research assistant for the life sciences. This plugin brings\ntogether literature search, data analysis pipelines,\nand scientific strategy — all in one place.\n```\n\n## Step 2: Check Available MCP Servers\n\nTest which MCP servers are connected by listing available tools. Group the results:\n\n**Literature & Data Sources:**\n- ~~literature database — biomedical literature search\n- ~~literature database — preprint access (biology and medicine)\n- ~~journal access — academic publications\n- ~~data repository — collaborative research data (Sage Bionetworks)\n\n**Drug Discovery & Clinical:**\n- ~~chemical database — bioactive compound database\n- ~~drug target database — drug target discovery platform\n- ClinicalTrials.gov — clinical trial registry\n- ~~clinical data platform — clinical trial site ranking and platform help\n\n**Visualization & AI:**\n- ~~scientific illustration — create scientific figures and diagrams\n- ~~AI research platform — AI for biology (histopathology, drug discovery)\n\nReport which servers are connected and which are not yet set up.\n\n## Step 3: Survey Available Skills\n\nList the analysis skills available in this plugin:\n\n| Skill | What It Does |\n|-------|-------------|\n| **Single-Cell RNA QC** | Quality control for scRNA-seq data with MAD-based filtering |\n| **scvi-tools** | Deep learning for single-cell omics (scVI, scANVI, totalVI, PeakVI, etc.) |\n| **Nextflow Pipelines** | Run nf-core pipelines (RNA-seq, WGS/WES, ATAC-seq) |\n| **Instrument Data Converter** | Convert lab instrument output to Allotrope ASM format |\n| **Scientific Problem Selection** | Systematic framework for choosing research problems |\n\n## Step 4: Optional Setup — Binary MCP Servers\n\nMention that two additional MCP servers are available as separate installations:\n\n- **~~genomics platform** — Access cloud analysis data and workflows\n  Install: Download `txg-node.mcpb` from https://github.com/10XGenomics/txg-mcp/releases\n- **~~tool database** (Harvard MIMS) — AI tools for scientific discovery\n  Install: Download `tooluniverse.mcpb` from https://github.com/mims-harvard/ToolUniverse/releases\n\nThese require downloading binary files and are optional.\n\n## Step 5: Ask How to Help\n\nAsk the researcher what they're working on today. Suggest starting points based on common workflows:\n\n1. **Literature review** — \"Search ~~literature database for recent papers on [topic]\"\n2. **Analyze sequencing data** — \"Run QC on my single-cell data\" or \"Set up an RNA-seq pipeline\"\n3. **Drug discovery** — \"Search ~~chemical database for compounds targeting [protein]\" or \"Find drug targets for [disease]\"\n4. **Data standardization** — \"Convert my instrument data to Allotrope format\"\n5. **Research strategy** — \"Help me evaluate a new project idea\"\n\nWait for the user's response and guide them to the appropriate tools and skills.",
  "applicable_domains": [
    "research",
    "science"
  ],
  "invocation": [
    "/start"
  ],
  "tags": [
    "bio-research",
    "anthropics",
    "knowledge-work"
  ],
  "authored_by": "anthropics",
  "source_url": "https://github.com/anthropics/knowledge-work-plugins/blob/main/bio-research/skills/start/SKILL.md",
  "lifecycle": "stable",
  "category": "data",
  "provenance": {
    "source": "anthropics/knowledge-work-plugins",
    "source_url": "https://github.com/anthropics/knowledge-work-plugins/blob/main/bio-research/skills/start/SKILL.md",
    "author": "Anthropic",
    "license": "Apache-2.0",
    "notes": "Imported by scripts/import-anthropic-skills.py."
  }
}