Single-Cell Intelligence Agent -- Documentation Index¶

Part of the Precision Intelligence Network — one of 11 specialized agents sharing a common molecular foundation within the HCLS AI Factory.

Version: 1.0.0 Date: 2026-03-22 Agent: Single-Cell Intelligence Agent Ports: API 8540 | UI 8130

Documentation Set¶

#	Document	Description	Audience
1	Production Readiness Report	25-section PRR covering architecture, collections, workflows, decision engines, security, testing, and go/no-go recommendation	Engineering, QA
2	Project Bible	Mission, problem statement, solution architecture, feature inventory, technical stack, data flow, quality gates, and roadmap	All stakeholders
3	Architecture Guide	Layered architecture, GPU acceleration pipeline, RAPIDS integration, TME classification pipeline, spatial deconvolution, RAG search architecture	Engineering
4	White Paper	Resolution gap in precision medicine, tumor heterogeneity, GPU necessity, clinical applications, foundation models	Executive, clinical
5	Deployment Guide	Standalone Docker Compose, integrated DGX Spark, manual development setup, configuration reference, monitoring, scaling	DevOps, engineering
6	Demo Guide	5 demos: cell type annotation, TME profiling, drug response, CAR-T validation, spatial analysis	Sales, clinical, demos
7	Learning Guide: Foundations	Single-cell primer: technologies, data formats (AnnData), analysis pipeline (QC to clustering to DE)	New team members
8	Learning Guide: Advanced	TME classification deep dive, subclonal architecture, spatial transcriptomics, trajectory inference, foundation models (scGPT/Geneformer), GPU benchmarks	Experienced analysts
9	Research Paper	Academic research paper on the agent's design and capabilities	Publications

Quick Reference¶

Agent Statistics¶

Metric	Value
Milvus collections	12
Analysis workflows	10
Decision support engines	4
Cell types in knowledge base	44
Drugs modeled	30
Marker genes	75
Immune signatures	10
Ligand-receptor pairs	25
Cancer TME atlas profiles	12
API endpoints	25
Test cases	~185
Source code lines	14,560

Port Map¶

Port	Service
8540	FastAPI REST API
8130	Streamlit UI
19530	Milvus (shared)
69530	Milvus (standalone)

Key Files¶

Path	Purpose
`config/settings.py`	All configuration with `SC_` env prefix
`src/agent.py`	Core reasoning engine
`src/collections.py`	12 Milvus collection schemas
`src/clinical_workflows.py`	10 analysis workflows
`src/decision_support.py`	4 clinical engines
`src/knowledge.py`	Domain knowledge base
`api/main.py`	FastAPI application
`app/sc_ui.py`	Streamlit UI
`docker-compose.yml`	Standalone deployment

HCLS AI Factory -- Single-Cell Intelligence Agent Documentation Index v1.0.0

Clinical Decision Support Disclaimer

This agent is a clinical decision support research tool. It is not FDA-cleared and is not intended as a standalone diagnostic device. All recommendations should be reviewed by qualified healthcare professionals. Apache 2.0 License.