Spatial Transcriptomics — Mode Router

Decision Tree

Route user requests to one of three personality modes. Detect intent from keywords in the user's natural language question, then load the corresponding mode file.

User Question
    │
    ├── Contains Socrates markers?
    │   "全新" "颠覆" "换思路" "unconventional" "breakthrough"
    │   "rethink" "from scratch" "无预设" "paradigm shift"
    │   "abandon standard" "completely new direction"
    │       → YES → Load modes/socrates.md
    │
    ├── Contains Plato markers?
    │   "新方法" "前沿" "cutting-edge" "recent" "improved"
    │   "最新" "更好的方法" "state of the art" "alternative"
    │   "compare methods" "beyond standard" "最新进展"
    │       → YES → Load modes/plato.md
    │
    ├── Contains Aristotle markers?
    │   "标准流程" "常规分析" "standard pipeline" "routine analysis"
    │   "best practice" "tried and tested" "gold standard"
    │   "recommended workflow" "standard preprocessing" "QC"
    │       → YES → Load modes/aristotle.md
    │
    └── No clear markers (DEFAULT)
            → Load modes/aristotle.md (safety-first)

Ambiguity resolution: When markers from multiple modes are present, use this priority: socrates > plato > aristotle. Novelty-seeking overrides safety defaults. If only "novel" appears without stronger markers, route to plato mode.

Mode Overview

Aristotle (modes/aristotle.md)

Standard, reproducible spatial transcriptomics pipelines using well-established tools (Scanpy, Squidpy, Seurat). Follows community-vetted best practices, built-in QC thresholds, and published workflows. Aristotle was the empiricist who classified all of nature — this mode inherits his systematic rigor. Appropriate for routine analysis, benchmarking, and when reproducibility is paramount. No experimental methods are recommended.

Plato (modes/plato.md)

Standard pipelines augmented with systematic literature search via BioMCP. Searches PubMed for recent methods (last 2 years), compares alternatives, and recommends improvements over the baseline pipeline. Plato was the dialectician who explored every possibility — this mode inherits his breadth. Useful when the user wants to know about newer approaches without abandoning the standard framework entirely.

Socrates (modes/socrates.md)

Question-driven reverse design. Starts from the user's biological question, then designs a custom analysis strategy from scratch — tool selection, parameter choices, and interpretation framework are all derived from the question rather than from a predefined pipeline. Socrates was the gadfly who questioned everything until truth emerged — this mode inherits his relentless curiosity. No preset assumptions about which tools should be used.

BioMCP Integration

This skill uses the biomcp_biomcp MCP tool for biomedical queries. All modes may invoke it, but Plato and Socrates modes rely on it heavily for literature-backed method discovery.

Usage rule: Always trigger BioMCP when the user asks about a specific gene, pathway, or disease context. For method discovery in Plato/Socrates modes, at least one BioMCP literature search is mandatory before recommending a pipeline.

Self-Evolution

This skill writes to ~/.spatial-transcriptomics-memory/ for persistent learning across sessions:

• Findings log: ~/.spatial-transcriptomics-memory/findings.jsonl — append insights from each analysis session (methods that worked, edge cases, platform-specific quirks).
• Method catalog: reference/methods-catalog.md — curated list of spatial methods with platform compatibility, performance notes, and citation anchors.
• Personality memory: Each mode file tracks its own session history in ~/.spatial-transcriptomics-memory/<mode>-sessions.jsonl (aristotle/plato/socrates) for context continuity.

Before starting any analysis, the skill should briefly scan the findings log for relevant past insights. After completing analysis, new findings are appended.

Code Templates

Reusable analysis templates are stored in templates/. These are Python scripts or Jupyter notebook stubs that each mode can customize:

Each template includes placeholder comments (# TODO: CONFIGURE) where mode-specific decisions are injected. Aristotle mode fills these with default values; Plato and Socrates modes replace them with literature-backed or question-driven choices.

File Map

spatial-transcriptomics/
├── SKILL.md                  ← THIS FILE (router)
├── modes/
│   ├── aristotle.md          ← Standard pipeline mode
│   ├── plato.md              ← Literature-augmented mode
│   └── socrates.md           ← Question-driven reverse design mode
├── reference/
│   └── methods-catalog.md    ← Curated spatial methods reference
├── templates/
│   ├── qc-template.py
│   ├── clustering-template.py
│   ├── svg-template.py
│   ├── deconv-template.py
│   ├── niche-template.py
│   └── viz-template.py
└── memory/                   ← Session-level scratch (not persisted)