Initialize the productivity system and open the dashboard. Use when setting up the plugin for the first time, bootstrapping working memory from your existing task list, or decoding the shorthand (nicknames, acronyms, project codenames) you use in your todos.

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) ~~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.mcpb from https://github.com/10XGenomics/txg mcp/releases ~~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. Step 5: Ask How to Help 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]" 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. 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.