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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.
npx claudepluginhub lohasle/knowledge-work-plugins --plugin bio-researchHow 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...
/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.
/analyzeALWAYS invoke this skill when a user wants to perform computational analysis on data in this repository. This skill loads project-specific analysis conventions, dataset registries, and methodology requirements (validation checks, sensitivity sweeps, null hypothesis testing) that are not available from general knowledge — you cannot do the analysis correctly without consulting it first. Trigger for: running any named analysis technique (clustering, PCA, UMAP, differential expression, survival analysis, dose-response, model fitting, time-series, batch correction, statistical tests), exploring or investigating patterns in data, continuing or extending a previous analysis, debugging or troubleshooting analytical results (wrong clusters, unexpected patterns, parameter tuning). The user's intent must be to computationally process or model data — not just read it, not just look at a file. Do NOT trigger for: reading or previewing data files without analysis, writing reports or documents, brainstorming ideas, setting up or initializing repositories, installing conventions, ingesting or importing data files, fixing code bugs unrelated to analytical results, or updating documentation.
/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.
Share bugs, ideas, or general feedback.
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.