cy-wali/start
bio-research/skills/start/SKILL.md
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.
tools
Updated Apr 4, 2026
$ install --global
skillsauthnpx skillsauth add cy-wali/knowledge startInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
Security Scan Results
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TrivyContainer and dependency vulnerability scanner
95%
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SemgrepStatic code analysis for vulnerabilities
95%
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mcp-scan (Snyk)Model Context Protocol security validation
95%
Skipped
Snyk (dep)Open source security scanning
50%
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Socket.devSupply chain security analysis
50%
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VirusTotalMulti-engine malware detection
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CrowdStrikeAdvanced threat intelligence
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OWASP Dep-Check
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Last scanned: Apr 4, 2026, 2:15 PM4.3s1 file scanned
SKILL.md
- 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.
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.mcpbfrom https://github.com/10XGenomics/txg-mcp/releases - ~~tool database (Harvard MIMS) — AI tools for scientific discovery
Install: Download
tooluniverse.mcpbfrom 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.
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