Mermaid Architect Guide

---
config:
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  theme: neutral
---
flowchart LR
    A[Raw Data] --> B[Preprocessing]
    B --> C[Feature Engineering]
    C --> D[Model Training]
    D --> E[Evaluation]
    E -->|Poor| C
    E -->|Good| F[Deployment]

C4Context
    title Research Platform - System Context

    Person(researcher, "Researcher", "Academic user conducting studies")
    Person(admin, "Platform Admin", "Manages skills and users")

    System(platform, "Wentor Platform", "AI-powered research assistant ecosystem")

    System_Ext(scholar, "OpenAlex", "Academic paper database")
    System_Ext(crossref, "CrossRef", "DOI resolution and metadata")
    System_Ext(github, "GitHub", "Code and skill repositories")

    Rel(researcher, platform, "Uses", "HTTPS")
    Rel(admin, platform, "Manages", "HTTPS")
    Rel(platform, scholar, "Queries papers", "REST API")
    Rel(platform, crossref, "Resolves DOIs", "REST API")
    Rel(platform, github, "Fetches skills", "REST API")

C4Container
    title Research Platform - Container View

    Person(researcher, "Researcher")

    Container_Boundary(platform, "Wentor Platform") {
        Container(web, "Web App", "React + UmiJS", "Browser-based UI")
        Container(api, "API Server", "FastAPI", "REST endpoints")
        Container(claw, "Research-Claw", "Node.js", "Local AI agent")
        ContainerDb(db, "Database", "PostgreSQL", "User data, skills, tokens")
        ContainerDb(cache, "Cache", "Redis", "Session and rate limit data")
    }

    System_Ext(llm, "LLM Provider", "Claude / GPT")

    Rel(researcher, web, "Browses", "HTTPS")
    Rel(researcher, claw, "Runs locally", "WS localhost")
    Rel(web, api, "Calls", "REST/JSON")
    Rel(api, db, "Reads/Writes", "SQL")
    Rel(api, cache, "Caches", "Redis protocol")
    Rel(claw, llm, "Sends prompts", "HTTPS")

flowchart TB
    subgraph ingestion ["Data Ingestion Layer"]
        direction LR
        A1[PubMed API] --> B1[Raw Store]
        A2[arXiv API] --> B1
        A3[CrossRef API] --> B1
    end

    subgraph processing ["Processing Pipeline"]
        direction LR
        C1[Text Extraction] --> C2[NER & Entity Linking]
        C2 --> C3[Citation Graph Construction]
        C3 --> C4[Embedding Generation]
    end

    subgraph serving ["Serving Layer"]
        direction LR
        D1[Search Index] --> D2[Recommendation Engine]
        D2 --> D3[REST API]
    end

    ingestion --> processing --> serving

flowchart TD
    Start([Begin Experiment]) --> Design[Study Design]
    Design --> IRB{IRB Approval?}
    IRB -->|Approved| Pilot[Pilot Study n=30]
    IRB -->|Revision needed| Design
    Pilot --> PilotCheck{Pilot Successful?}
    PilotCheck -->|Yes| FullStudy[Full Study n=300]
    PilotCheck -->|No| Redesign[Revise Protocol]
    Redesign --> Pilot
    FullStudy --> Analysis[Statistical Analysis]
    Analysis --> Results{Significant?}
    Results -->|p < 0.05| Write[Write Manuscript]
    Results -->|p >= 0.05| Explore[Exploratory Analysis]
    Explore --> Write
    Write --> Submit([Submit to Journal])

stateDiagram-v2
    [*] --> Ideation
    Ideation --> ProposalDrafting : Concept validated

    state ProposalDrafting {
        [*] --> Writing
        Writing --> InternalReview
        InternalReview --> Writing : Revisions needed
        InternalReview --> Ready : Approved
    }

    ProposalDrafting --> Submitted : Submit to funder
    Submitted --> UnderReview : Acknowledged
    UnderReview --> Funded : Award
    UnderReview --> Rejected : Decline
    Rejected --> Ideation : Revise concept
    Funded --> Active : Project kickoff
    Active --> Reporting : Milestone due
    Reporting --> Active : Report accepted
    Active --> Completed : All deliverables met
    Completed --> [*]

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flowchart LR
    A[Input] --> B[Process] --> C[Output]

# Install Mermaid CLI
npm install -g @mermaid-js/mermaid-cli

# Render to SVG
mmdc -i architecture.mmd -o architecture.svg -t neutral

# Render with hand-drawn look
mmdc -i architecture.mmd -o sketch.svg --configFile mermaid-config.json