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From bio-research
Orients bio-researchers with welcome message, checks connected MCP servers, lists analysis skills like scvi-tools and Nextflow, and suggests workflows.
How this command is triggered — by the user, by Claude, or both
Slash command
/bio-research:startThe summary Claude sees in its command listing — used to decide when to auto-load this command
# 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: ## 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...
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.
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.
Test which MCP servers are connected by listing available tools. Group the results:
Literature & Data Sources:
Drug Discovery & Clinical:
Visualization & AI:
Report which servers are connected and which are not yet set up.
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 |
Mention that two additional MCP servers are available as separate installations:
txg-node.mcpb from https://github.com/10XGenomics/txg-mcp/releasestooluniverse.mcpb from https://github.com/mims-harvard/ToolUniverse/releasesThese require downloading binary files and are optional.
Ask the researcher what they're working on today. Suggest starting points based on common workflows:
Wait for the user's response and guide them to the appropriate tools and skills.
npx claudepluginhub lohasle/knowledge-work-plugins --plugin bio-research/researchConducts a multi-database scientific research investigation using ToolUniverse, calling tools to look up specific claims, cross-validate, and report honest INDETERMINATE results when evidence is insufficient.
/run-demoRuns ClawBio skill demo with built-in sample data for specified skill (e.g., pharmgx, scrna), displays generated report, explains results, and opens figures. Lists available demos if unspecified.
/search-encodeSearches ENCODE experiments by assay, organ, biosample, or target using encode_search_experiments with filters. Supports facets for exploration and metadata discovery.
/choose-skillMaps a user's natural-language task to the best-matching Research Agora skills, presenting top recommendations with confidence scores and example invocations.
/aboutShows interactive documentation for Research System plugin. Reads README.md, presents topic options like Quick Start or Commands, displays selected section, and offers to continue.
/analyzeStarts or continues a computational analysis project, loading project-specific conventions, dataset registries, and methodology requirements for techniques like clustering, PCA, and statistical tests.