Merge pull request #2 from anthropics/bio_fix

Updating bio-research plugin

Author: mattpic-ant

bio-research/README.md

@@ -2,7 +2,7 @@
 
 Connect to preclinical research tools and databases (literature search, genomics analysis, target prioritization) to accelerate early-stage life sciences R&D. Use with [Cowork](https://claude.com/product/cowork) or install directly in Claude Code.
 
-This plugin consolidates 10 MCP server integrations and 6 analysis skills into a single package for life science researchers.
+This plugin consolidates 10 MCP server integrations and 5 analysis skills into a single package for life science researchers.
 
 ## What's Included
 
@@ -44,9 +44,6 @@ Run nf-core bioinformatics pipelines on local or public GEO/SRA sequencing data:
 - **sarek** — Germline and somatic variant calling (WGS/WES)
 - **atacseq** — Chromatin accessibility analysis
 
-#### Clinical Trial Protocol
-Generate FDA/NIH-compliant clinical trial protocols for medical devices or drugs. Includes research mode (literature + regulatory analysis) and full protocol generation with waypoint-based architecture.
-
 #### Instrument Data to Allotrope
 Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) format. Supports 40+ instrument types including cell counters, spectrophotometers, plate readers, qPCR, and chromatography systems.
 
@@ -77,9 +74,6 @@ Download public data from GEO/SRA, run nf-core pipelines (RNA-seq, variant calli
 **Drug Discovery**
 Search ~~chemical database for bioactive compounds, use ~~drug target database for target prioritization, and review clinical trial data.
 
-**Clinical Trial Design**
-Research similar trials and FDA guidance, then generate a complete protocol document with statistical analysis.
-
 **Research Strategy**
 Pitch a new idea, troubleshoot a stuck project, or evaluate strategic decisions using the scientific problem selection framework.
 

bio-research/commands/start.md

@@ -16,7 +16,7 @@ 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, clinical trial tools,
+together literature search, data analysis pipelines,
 and scientific strategy — all in one place.
 ```
 
@@ -51,7 +51,6 @@ List the analysis skills available in this plugin:
 | **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) |
-| **Clinical Trial Protocol** | Generate FDA/NIH-compliant clinical trial protocols |
 | **Instrument Data Converter** | Convert lab instrument output to Allotrope ASM format |
 | **Scientific Problem Selection** | Systematic framework for choosing research problems |
 
@@ -73,8 +72,7 @@ Ask the researcher what they're working on today. Suggest starting points based
 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. **Clinical trial design** — "Help me design a clinical trial protocol for [intervention]"
-5. **Data standardization** — "Convert my instrument data to Allotrope format"
-6. **Research strategy** — "Help me evaluate a new project idea"
+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.