PF-Atlas Open Research API

Deep biological simulation modeling 12 cell types and 10 signaling pathways. Tracks FVC, AEC2 stem cells, senescent burden, and ECM stiffness over time.

Request Body

{
  "species": "human",       // "human" or "mouse"
  "drugs": ["nintedanib", "quercetin"],
  "duration": 24,            // months (max 60)
  "fvc_start": 50            // baseline FVC%
}

Response

{
  "trajectory": [
    { "day": 0, "cells": { "aec2": 0.35, "senAec2": 0.12 }, "tissue": { "fvc": 0.50, "ecmStiffness": 0.65 } },
    ...
  ],
  "finalFVC": 58.3,
  "finalAEC2": 0.42,
  "finalSen": 0.06,
  "finalECM": 0.51,
  "isRegeneration": true
}

cURL

curl -X POST https://pf-atlas.com/api/v1/simulate \
  -H "Content-Type: application/json" \
  -d '{"species":"human","drugs":["nintedanib","quercetin"],"duration":24,"fvc_start":50}'

Full biosimulation engine modeling fibroblasts, AEC2 cells, macrophages, senescent cells, and their signaling interactions.

Request Body

{
  "species": "human",
  "drugs": ["pirfenidone", "dasatinib"],
  "months": 24,
  "fvc": 50
}

Response

{
  "ok": true,
  "snapshots": [ ... ],
  "species": "human",
  "drugs": ["pirfenidone", "dasatinib"]
}

cURL

curl -X POST https://pf-atlas.com/api/biosim \
  -H "Content-Type: application/json" \
  -d '{"species":"human","drugs":["pirfenidone","dasatinib"],"months":24,"fvc":50}'

Runs an ODE-based FVC trajectory simulation comparing all available treatments against natural disease progression. Returns month-by-month FVC values for each treatment option.

Request Body

{
  "initialFVC": 75,
  "diseaseRate": 1.0,
  "hasTERT": false,
  "months": 24,
  "treatment": "nintedanib"
}

Response

{
  "ok": true,
  "comparison": [
    {
      "key": "nintedanib",
      "label": "Nintedanib",
      "data": [75, 74.2, ...],
      "metrics": { "finalFVC": 68.5, "decline": -6.5 },
      "highlighted": true
    }, ...
  ],
  "treatments": { ... }
}

cURL

curl -X POST https://pf-atlas.com/api/simulate \
  -H "Content-Type: application/json" \
  -d '{"initialFVC":75,"diseaseRate":1.0,"hasTERT":false,"months":24,"treatment":"nintedanib"}'

Returns every modeled drug with its mechanism of action, pharmacokinetic parameters, and target pathways. Use these drug keys in simulation endpoints.

Response

{
  "drugs": [
    {
      "key": "nintedanib",
      "name": "Nintedanib (Ofev)",
      "mechanism": "Triple TKI (VEGFR/FGFR/PDGFR)",
      "halfLife": 10,
      ...
    }, ...
  ]
}

cURL

curl https://pf-atlas.com/api/v1/drugs

Returns all tracked IPF treatments ranked by composite score, including mechanism details, evidence levels, development stage, and risk profiles.

Response

{
  "rows": [
    {
      "id": 1,
      "name": "PLN-74809 (Bexotegrast)",
      "mechanism": "Dual integrin inhibitor",
      "evidence_level": "Level 2",
      "stage": "Phase II",
      "risk": "Low",
      "score": 92.5
    }, ...
  ]
}

cURL

curl https://pf-atlas.com/api/treatments

Returns the top 10 highest-scoring drug combinations found by the genetic algorithm solver. The solver runs continuously, evolving populations of candidate combinations.

Response

{
  "results": [
    {
      "id": 42,
      "species": "human",
      "drugs": "[\"nintedanib\",\"quercetin\",\"rapamycin\"]",
      "fvc_start": 50,
      "fvc_end": 62.3,
      "score": 87.5,
      "is_regen": 1
    }, ...
  ]
}

cURL

curl https://pf-atlas.com/api/v1/solver/best

Returns current genetic algorithm solver state including generation count, total combinations tested, best score, and top 10 results for both human and mouse species.

Response

{
  "generation": 1523,
  "totalTested": 45690,
  "totalSaved": 312,
  "bestScore": 91.2,
  "top10": [ ... ],
  "humanBest": { ... },
  "mouseBest": { ... }
}

cURL

curl https://pf-atlas.com/api/solver/status

Returns the day-by-day simulation trajectory for the best drug combination. Includes full cell counts, tissue state, and signaling at each time point.

Query Parameters

species=human  // "human" or "mouse" (default: human)

Response

{
  "ok": true,
  "snapshots": [ ... ],
  "drugs": ["nintedanib", "quercetin", "rapamycin"],
  "species": "human"
}

cURL

curl "https://pf-atlas.com/api/solver/trajectory?species=human"

Query the indexed research paper database. Supports pagination, domain filtering, and full-text search across titles and authors.

Query Parameters

page=1           // Page number (default: 1)
limit=30          // Results per page (default: 30)
domain=USA        // Filter by country/domain
search=fibroblast // Search title or authors

Response

{
  "rows": [
    {
      "id": 1,
      "pubmed_id": "38456789",
      "title": "Novel anti-fibrotic targets in IPF...",
      "authors": "Smith J, Chen W",
      "journal": "Am J Respir Crit Care Med",
      "year": 2025,
      "domain": "USA",
      "score": 85.2
    }, ...
  ],
  "total": 1247,
  "page": 1,
  "limit": 30,
  "domains": ["USA", "China", "Japan", ...]
}

cURL

curl "https://pf-atlas.com/api/papers?page=1&limit=10&search=senolytic"

Returns paper counts grouped by country/domain, sorted by volume.

Response

{
  "countries": [
    { "domain": "USA", "cnt": 312 },
    { "domain": "China", "cnt": 198 },
    ...
  ]
}

cURL

curl https://pf-atlas.com/api/papers/by-country

Fetches the full abstract from PubMed for a given PubMed ID. Only works for papers with valid PubMed IDs (not seed/bioRxiv/etc).

Response

{
  "abstract": "Background: Idiopathic pulmonary fibrosis...",
  "pubmed_id": "38456789"
}

cURL

curl https://pf-atlas.com/api/paper/38456789/abstract

Returns all tracked IPF clinical trials from ClinicalTrials.gov. Filterable by status and phase.

Query Parameters

status=Recruiting   // Filter by trial status
phase=Phase 2        // Filter by phase

Response

{
  "rows": [
    {
      "id": 1,
      "nct_id": "NCT05032456",
      "title": "A Study of Bexotegrast in IPF",
      "status": "Recruiting",
      "phase": "Phase 2",
      "mechanism": "Integrin inhibitor",
      "drug": "PLN-74809",
      "sponsor": "Pliant Therapeutics"
    }, ...
  ],
  "total": 45
}

cURL

curl "https://pf-atlas.com/api/trials?phase=Phase%202"

Returns the latest AI-generated discoveries and insights from cross-disease analysis, solver breakthroughs, and scan results. Translated into EN/RU/HE.

Response

{
  "rows": [
    {
      "id": 1,
      "type": "cross_disease",
      "title": "GLP-1 agonists show anti-fibrotic potential",
      "body": "...",
      "title_ru": "...",
      "title_he": "..."
    }, ...
  ],
  "scanRunning": false,
  "lastScan": { ... },
  "nextScanTs": 1718150400
}

cURL

curl https://pf-atlas.com/api/discoveries

Returns AI-generated cross-domain research hypotheses, each combining two mechanisms from different fields with confidence scoring.

Response

{
  "rows": [
    {
      "id": 1,
      "title": "Senolytic-WNT sequential therapy",
      "description": "Clear senescent cells first, then...",
      "mechanism_a": "Senolytics",
      "mechanism_b": "WNT agonists",
      "confidence_score": 0.72,
      "biological_plausibility": 0.85,
      "technical_feasibility": 0.60,
      "estimated_timeline": "3-5 years"
    }, ...
  ]
}

cURL

curl https://pf-atlas.com/api/hypotheses

Upload wet lab or clinical results. The system automatically runs the same drug combination through its simulation engine and compares predicted vs actual FVC, calculating model accuracy.

Request Body

{
  "experiment_type": "cell_culture",  // "cell_culture", "mouse", or "clinical"
  "drugs": ["nintedanib", "pirfenidone"],
  "result_fvc": 62.5,
  "result_notes": "3-month cell culture study",
  "researcher_email": "researcher@university.edu"
}

Response

{
  "id": 7,
  "simulated_fvc": 59.8,
  "actual_fvc": 62.5,
  "accuracy": 97.3
}

cURL

curl -X POST https://pf-atlas.com/api/v1/lab-results \
  -H "Content-Type: application/json" \
  -d '{"experiment_type":"cell_culture","drugs":["nintedanib"],"result_fvc":62.5,"result_notes":"test"}'

Returns all uploaded lab results alongside their simulated predictions and accuracy scores.

Response

{
  "results": [
    {
      "id": 1,
      "experiment_type": "cell_culture",
      "drugs": "[\"nintedanib\"]",
      "result_fvc": 62.5,
      "simulated_fvc": 59.8,
      "accuracy": 97.3
    }, ...
  ]
}

cURL

curl https://pf-atlas.com/api/v1/lab-results

Models pharmacokinetic interactions between IPF drugs. Checks CYP enzyme interactions (CYP3A4, CYP1A2, CYP2C9), protein binding competition, and additive toxicity risks.

Request Body

{
  "drugs": ["nintedanib", "pirfenidone", "rapamycin"]
}

Response

{
  "interactions": [
    {
      "drugA": "nintedanib",
      "drugB": "pirfenidone",
      "severity": "moderate",
      "mechanism": "CYP3A4 competition",
      "warning": "Monitor liver enzymes"
    }, ...
  ],
  "overallRisk": "moderate"
}

cURL

curl -X POST https://pf-atlas.com/api/interactions \
  -H "Content-Type: application/json" \
  -d '{"drugs":["nintedanib","pirfenidone","rapamycin"]}'

Calculates cumulative organ toxicity scores for a drug combination over a specified duration, adjusted for patient age.

Request Body

{
  "drugs": ["nintedanib", "pirfenidone"],
  "duration": 720,   // days (default: 720)
  "age": 65            // patient age (default: 65)
}

Response

{
  "liver": 0.35,
  "kidney": 0.18,
  "cardiac": 0.12,
  "gi": 0.42,
  "overallToxicity": 0.27
}

cURL

curl -X POST https://pf-atlas.com/api/toxicity \
  -H "Content-Type: application/json" \
  -d '{"drugs":["nintedanib","pirfenidone"],"duration":720,"age":65}'

Calculates a composite quality of life score that balances FVC improvement against drug side-effect burden and toxicity accumulation.

Request Body

{
  "fvc": 55,
  "drugs": ["nintedanib", "quercetin"]
}

Response

{
  "qolScore": 72.5,
  "fvcContribution": 55,
  "toxicityPenalty": -8.2,
  "drugBurdenPenalty": -4.3
}

cURL

curl -X POST https://pf-atlas.com/api/qol \
  -H "Content-Type: application/json" \
  -d '{"fvc":55,"drugs":["nintedanib","quercetin"]}'

Predicts binding affinity between drugs and their IPF-relevant protein targets. Useful for understanding drug potency and potential synergy at the molecular level.

Request Body

{
  "drugs": ["nintedanib", "bexotegrast"]
}

Response

{
  "bindings": [
    {
      "drug": "nintedanib",
      "targets": [
        { "protein": "VEGFR2", "affinity": 0.89 },
        { "protein": "FGFR1", "affinity": 0.76 }
      ]
    }, ...
  ]
}

cURL

curl -X POST https://pf-atlas.com/api/binding \
  -H "Content-Type: application/json" \
  -d '{"drugs":["nintedanib","bexotegrast"]}'

Scores the combined evidence for a multi-drug combination, considering clinical trial data, preclinical studies, and mechanistic plausibility.

Request Body

{
  "drugs": ["nintedanib", "quercetin", "metformin"]
}

cURL

curl -X POST https://pf-atlas.com/api/evidence/combo \
  -H "Content-Type: application/json" \
  -d '{"drugs":["nintedanib","quercetin","metformin"]}'

Returns the evidence profile for a single drug, including trial results, publication count, and confidence levels.

cURL

curl https://pf-atlas.com/api/evidence/nintedanib

Generates a week-by-week phased treatment protocol. The sequencing engine determines optimal drug ordering (e.g., senolytics first to clear damaged cells, then growth factors for regeneration).

Request Body

{
  "drugs": ["dasatinib", "quercetin", "nintedanib"],
  "fvc": 50,
  "months": 24
}

cURL

curl -X POST https://pf-atlas.com/api/protocol/sequential \
  -H "Content-Type: application/json" \
  -d '{"drugs":["dasatinib","quercetin","nintedanib"],"fvc":50,"months":24}'

Tests all possible sequencing orders for a given drug set and returns the one producing the best FVC outcome.

Request Body

{
  "drugs": ["nintedanib", "quercetin", "rapamycin"],
  "fvc": 50
}

cURL

curl -X POST https://pf-atlas.com/api/protocol/optimize \
  -H "Content-Type: application/json" \
  -d '{"drugs":["nintedanib","quercetin","rapamycin"],"fvc":50}'

Compares the outcome of taking all drugs simultaneously versus introducing them in a phased sequence.

Request Body

{
  "drugs": ["nintedanib", "pirfenidone"],
  "fvc": 50
}

cURL

curl -X POST https://pf-atlas.com/api/protocol/compare \
  -H "Content-Type: application/json" \
  -d '{"drugs":["nintedanib","pirfenidone"],"fvc":50}'

Creates a digital twin patient profile from clinical parameters and returns risk stratification. The twin models fibroblast density, collagen deposition, AEC2 count, FVC trajectory, and immune populations.

Request Body

{
  "age": 65,
  "fvc": 55,
  "dlco": 40,
  "spo2": 92,
  "smoker": false,
  "familyHistory": false,
  "comorbidities": ["GERD"]
}

Response

{
  "profile": { "age": 65, "fvc": 55, ... },
  "stratification": {
    "riskGroup": "high",
    "predictedDecline": -8.2,
    "recommendedApproach": "aggressive"
  }
}

cURL

curl -X POST https://pf-atlas.com/api/digital-twin \
  -H "Content-Type: application/json" \
  -d '{"age":65,"fvc":55,"dlco":40,"spo2":92}'

Runs the genetic algorithm solver personalized to a specific patient profile. Returns the best drug combination tailored to their exact clinical parameters.

Request Body

{
  "age": 65,
  "fvc": 55,
  "dlco": 40,
  "spo2": 92,
  "generations": 50   // solver iterations (default: 50)
}

Response

{
  "profile": { ... },
  "result": {
    "bestCombo": ["nintedanib", "quercetin", "rapamycin"],
    "finalFVC": 62.1,
    "score": 88.4
  },
  "report": "Personalized analysis report..."
}

cURL

curl -X POST https://pf-atlas.com/api/digital-twin/solve \
  -H "Content-Type: application/json" \
  -d '{"age":65,"fvc":55,"dlco":40,"spo2":92,"generations":50}'

Generates and simulates a virtual cohort of IPF patients with varied clinical profiles. Useful for understanding population-level treatment effects.

Query Parameters

n=50  // Cohort size (default: 50, max: 200)

cURL

curl "https://pf-atlas.com/api/cohort?n=20"

Simulates fibrosis progression across 5 spatial zones of the lung (upper, middle, lower, peripheral, subpleural). Each zone has independent fibrosis rates and drug delivery characteristics.

Request Body

{
  "fvc": 50,
  "drugs": ["nintedanib", "pirfenidone"],
  "duration": 720   // days (default: 720)
}

cURL

curl -X POST https://pf-atlas.com/api/spatial-model \
  -H "Content-Type: application/json" \
  -d '{"fvc":50,"drugs":["nintedanib","pirfenidone"],"duration":720}'

Estimates biological (epigenetic) age based on chronological age and cellular state parameters. IPF patients typically show accelerated biological aging in lung tissue.

Request Body

{
  "chronologicalAge": 65,
  "cellState": {
    "senescence": 0.15,
    "telomereLength": 0.6,
    "dnaRepair": 0.7
  }
}

cURL

curl -X POST https://pf-atlas.com/api/epigenetic-age \
  -H "Content-Type: application/json" \
  -d '{"chronologicalAge":65,"cellState":{"senescence":0.15,"telomereLength":0.6}}'

Predicts how a given cellular state will transition under a specified intervention. Models transitions between healthy AEC2, senescent, and myofibroblast states.

Request Body

{
  "currentState": {
    "aec2": 0.35,
    "senescent": 0.15,
    "myofibroblast": 0.30
  },
  "intervention": "dasatinib"
}

cURL

curl -X POST https://pf-atlas.com/api/cell-transition \
  -H "Content-Type: application/json" \
  -d '{"currentState":{"aec2":0.35,"senescent":0.15,"myofibroblast":0.30},"intervention":"dasatinib"}'

Ask any question about IPF and receive an AI-generated answer in plain language. Supports English, Russian, and Hebrew. Optionally include patient context for personalized responses.

Request Body

{
  "message": "What are the latest treatment options for IPF?",
  "lang": "en",            // "en", "ru", or "he"
  "patient": {              // optional patient context
    "name": "John",
    "fvc": 55,
    "dlco": 40,
    "spo2": 92,
    "currentTreatment": "nintedanib"
  }
}

Response

{
  "ok": true,
  "text": "The most important treatment options for IPF right now are..."
}

cURL

curl -X POST https://pf-atlas.com/api/chat \
  -H "Content-Type: application/json" \
  -d '{"message":"What is nintedanib?","lang":"en"}'

Takes a drug combination and its simulation results, then uses AI to explain the synergy in plain language. Identifies which cascade steps each drug blocks and what gaps remain.

Request Body

{
  "combo": ["nintedanib", "quercetin", "rapamycin"],
  "fvc": 62.3,
  "aec2": 0.42,
  "sen": 0.06,
  "ecm": 0.51,
  "lang": "en"
}

Response

{
  "ok": true,
  "text": "This combination works well because nintedanib blocks..."
}

cURL

curl -X POST https://pf-atlas.com/api/explain-combo \
  -H "Content-Type: application/json" \
  -d '{"combo":["nintedanib","quercetin"],"fvc":58,"aec2":0.4,"sen":0.08,"ecm":0.55,"lang":"en"}'

Provide the current top-performing combinations and the full drug pool. AI will suggest a novel combination designed to outperform all existing ones by covering all 7 fibrosis cascade steps.

Request Body

{
  "topCombos": [
    { "names": ["nintedanib", "quercetin"], "fvc": 58.3 }
  ],
  "pool": ["nintedanib", "pirfenidone", "quercetin", "rapamycin", "metformin"]
}

Response

{
  "ok": true,
  "combo": ["nintedanib", "quercetin", "rapamycin", "metformin"]
}

cURL

curl -X POST https://pf-atlas.com/api/suggest-combo \
  -H "Content-Type: application/json" \
  -d '{"topCombos":[{"names":["nintedanib","quercetin"],"fvc":58}],"pool":["nintedanib","pirfenidone","quercetin","rapamycin","metformin"]}'

Upload a chest CT scan or X-ray as base64 and receive AI-powered analysis of pulmonary fibrosis findings, severity scoring, and clinical implications.

Request Body

{
  "imageBase64": "data:image/jpeg;base64,/9j/4AAQ...",
  "mediaType": "image/jpeg",  // default: "image/jpeg"
  "notes": "Patient with progressive dyspnea"
}

Response

{
  "ok": true,
  "ai": true,
  "imageType": "HRCT Chest",
  "severity": "Moderate",
  "findings": ["Bilateral honeycombing", ...],
  "clinicalImplications": "...",
  "recommendedSteps": ["PFT recommended", ...],
  "disclaimer": "AI analysis only. Clinical correlation required."
}

cURL

curl -X POST https://pf-atlas.com/api/analyze-scan \
  -H "Content-Type: application/json" \
  -d '{"imageBase64":"BASE64_DATA_HERE","mediaType":"image/jpeg","notes":"progressive dyspnea"}'

Generates a personalized treatment protocol using AI analysis of patient parameters. Combines simulation data with clinical reasoning to produce a recommended treatment plan.

Request Body

{
  "fvc": 55,
  "dlco": 40,
  "age": 65,
  "hasTERT": false,
  "diseaseRate": 1.0,
  "currentTreatment": "nintedanib",
  "comorbidities": ["GERD", "hypertension"]
}

Response

{
  "ok": true,
  "ai": true,
  "primaryTreatment": "nintedanib",
  "addOns": ["quercetin", "NMN"],
  "monitoring": "PFT every 3 months",
  "simulation": { "best": "combo_advanced", "finalFVC": 62.1 }
}

cURL

curl -X POST https://pf-atlas.com/api/protocol \
  -H "Content-Type: application/json" \
  -d '{"fvc":55,"dlco":40,"age":65,"diseaseRate":1.0,"currentTreatment":"nintedanib"}'

Returns the latest 200 forum posts from the IPF patient community. Posts can be in English, Russian, or Hebrew.

Response

[
  {
    "id": 1,
    "author": "Anonymous",
    "message": "Has anyone tried quercetin supplements?",
    "parent_id": 0,
    "created_at": 1718150400
  }, ...
]

cURL

curl https://pf-atlas.com/api/forum

Create a new forum post or reply. No registration required. Posts are limited to 2,000 characters.

Request Body

{
  "author": "John",          // optional, default: "Anonymous"
  "message": "My experience with nintedanib...",
  "parent_id": 0,             // 0 for new post, post ID for reply
  "lang": "en"                // "en", "ru", or "he"
}

Response

{
  "ok": true,
  "id": 42
}

cURL

curl -X POST https://pf-atlas.com/api/forum \
  -H "Content-Type: application/json" \
  -d '{"author":"Researcher","message":"Interesting findings on quercetin","lang":"en"}'

Upvote a forum post by ID. Replace :id with the post ID.

cURL

curl -X POST https://pf-atlas.com/api/forum/1/upvote

Researchers can claim interest in specific research topics or agent domains for collaboration. This helps coordinate global research efforts.

Request Body

{
  "researcher_name": "Dr. Jane Smith",
  "researcher_email": "jane@university.edu",
  "institution": "MIT",
  "agent_id": 5,
  "topic": "Senolytic therapy in IPF",
  "claim_type": "watching",    // "watching" or "active"
  "notes": "Running related clinical trial"
}

cURL

curl -X POST https://pf-atlas.com/api/collaborate/claim \
  -H "Content-Type: application/json" \
  -d '{"researcher_name":"Dr. Smith","topic":"Senolytic therapy","claim_type":"watching"}'

Returns all research topic claims from collaborating researchers worldwide.

cURL

curl https://pf-atlas.com/api/collaborate/claims