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Replace ~~placeholder strings with readable tool names in user-facing text #89

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Replace ~~placeholder strings with readable tool names in user-facing text #89

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25 changes: 12 additions & 13 deletions bio-research/commands/start.md
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Expand Up @@ -25,20 +25,19 @@ and scientific strategy — all in one place.
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)
- PubMed (~~literature) — biomedical literature search
- bioRxiv (~~literature) — preprint access (biology and medicine)
- Wiley Scholar Gateway (~~journal access) — academic publications
- Synapse (~~data repository) — collaborative research data (Sage Bionetworks)

**Drug Discovery & Clinical:**
- ~~chemical database — bioactive compound database
- ~~drug target database — drug target discovery platform
- ChEMBL (~~chemical database) — bioactive compound database
- Open Targets (~~drug targets) — 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)
- BioRender (~~scientific illustration) — create scientific figures and diagrams
- Owkin (~~AI research) — AI for biology (histopathology, drug discovery)

Report which servers are connected and which are not yet set up.

Expand All @@ -58,9 +57,9 @@ List the analysis skills available in this plugin:

Mention that two additional MCP servers are available as separate installations:

- **~~genomics platform** — Access cloud analysis data and workflows
- **10x Genomics** (~~genomics platform) — Access cloud analysis data and workflows
Install: Download `txg-node.mcpb` from https://github.com/10XGenomics/txg-mcp/releases
- **~~tool database** (Harvard MIMS) — AI tools for scientific discovery
- **ToolUniverse** (~~tool database, Harvard MIMS) — AI tools for scientific discovery
Install: Download `tooluniverse.mcpb` from https://github.com/mims-harvard/ToolUniverse/releases

These require downloading binary files and are optional.
Expand All @@ -69,9 +68,9 @@ These require downloading binary files and are optional.

Ask the researcher what they're working on today. Suggest starting points based on common workflows:

1. **Literature review** — "Search ~~literature database for recent papers on [topic]"
1. **Literature review** — "Search PubMed 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]"
3. **Drug discovery** — "Search ChEMBL for compounds targeting [protein]" or "Find drug targets for [disease]"
4. **Data standardization** — "Convert my instrument data to Allotrope format"
5. **Research strategy** — "Help me evaluate a new project idea"

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5 changes: 3 additions & 2 deletions enterprise-search/commands/search.md
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Expand Up @@ -25,9 +25,10 @@ Before searching, determine which MCP sources are available. Attempt to identify
If no MCP sources are connected:
```
To search across your tools, you'll need to connect at least one source.
Check your MCP settings to add ~~chat, ~~email, ~~cloud storage, or other tools.
Check your MCP settings to add a chat tool (e.g. Slack), email, cloud storage, or other tools.

Supported sources: ~~chat, ~~email, ~~cloud storage, ~~project tracker, ~~CRM, ~~knowledge base,
Supported sources: chat (e.g. Slack), email (e.g. Microsoft 365), cloud storage,
project tracker (e.g. Jira), CRM, knowledge base (e.g. Notion),
and any other MCP-connected service.
```

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4 changes: 2 additions & 2 deletions sales/skills/draft-outreach/SKILL.md
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Expand Up @@ -100,7 +100,7 @@ Research first, then draft. This skill never sends generic outreach - it always

## Email Draft Status

[Draft created - check ~~email]
[Draft created - check your email client]
[Email not connected - copy email above]
[No email found - use LinkedIn approach]

Expand Down Expand Up @@ -436,5 +436,5 @@ Best,
---

## Email Draft Status
Draft created - check ~~email
Draft created - check your email client
```