🧬 BioBots

Bioprinting computation toolkit & analysis platform

Material calculations · Rheology modeling · GCode analysis · Cell viability estimation · Cross-linking kinetics · 87 interactive tools

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📑 Table of Contents

• Quick Start
• What's Inside
• Live Demo — 87 Analysis Tools
• SDK — npm Package
• REST API
• Architecture
• Development
• Deployment
• Troubleshooting
• Contributing
• License

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⚡ Quick Start

All 87 analysis tools run entirely in your browser — no backend, no install, no dependencies:

→ Open the Dashboard

Start with:

• 📊 Data Explorer — histograms and scatter plots with regression
• 🎯 Quality Control — quality grading and optimal parameters
• ⚙️ Parameter Optimizer — find optimal parameters for any target metric
• 📋 Data Table — sortable, filterable data browser with CSV export

Or install the SDK:

npm install @sauravbhattacharya001/biobots

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📦 What's Inside

Component	Description
87 Browser Tools	Interactive analysis, visualization, and lab management tools — zero dependencies, pure client-side
80 SDK Factories	Node.js computation modules for material calc, rheology, GCode, viability, and more
REST API	ASP.NET Web API for querying bioprint statistics (11 metrics × 3 comparisons × 3 aggregations)
150 Test Suites	5,668 Jest tests covering SDK modules and analysis tools
.NET Models	NuGet package with data model classes for integration
Docker	Containerized deployment via GitHub Container Registry

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🌐 Live Demo — 87 Analysis Tools

All tools are deployed at sauravbhattacharya001.github.io/BioBots and render entirely client-side using Canvas API.

🔬 Core Analysis (8 tools)

Tool	Description
📊 Data Explorer	Histograms, scatter plots, regression, summary statistics
🔬 Print Comparison	Side-by-side comparison of 2–4 prints with radar charts
🎯 Quality Control	Quality grading (A–F), correlation heatmap, optimal parameters
🔍 Anomaly Detector	Z-Score and IQR outlier detection with severity classification
🔗 Cluster Analysis	K-means clustering with auto-k detection and silhouette scores
⚙️ Parameter Optimizer	Find optimal parameters for any target metric
📈 Trend Analysis	Moving averages, regression, metric correlations
📊 Correlation	Pairwise metric correlation matrix and insights

📊 Statistical & Process Control (8 tools)

Tool	Description
📊 SPC Charts	X-bar/R statistical process control charts
📊 Pareto Analysis	Multi-objective Pareto frontier visualization
🎛️ Sensitivity Analysis	Tornado charts, parameter impact ranking
📐 Design of Experiments	Parameter space coverage, gap analysis
📊 Statistics	Hypothesis testing and statistical calculator
📊 Reproducibility	Print reproducibility scoring
📉 Drift Detector	Parameter drift detection across runs
📊 Coverage Tracker	Parameter space coverage analysis

🧬 Bioink & Materials (9 tools)

Tool	Description
🧪 Bioink Calculator	Volume, cost, and time estimation for bioink preparations
🧪 Bioink Mixer	Multi-component mixing ratio optimization
🧪 Rheology Modeler	Power-law, Carreau, Herschel-Bulkley viscosity models
🧪 Materials Database	Bioink material properties and selection guide
🧫 Bioink Database	Searchable bioink properties with comparison
🧪 Compatibility Matrix	Material pairing compatibility matrix
🧫 Material Substitution	Smart material substitution recommendations
⏳ Shelf Life	Bioink stability and expiry tracking
📐 Standard Curve	Standard curve calculator for calibration data

🏗️ Print Setup & Design (8 tools)

Tool	Description
🏗️ Scaffold Designer	3D scaffold design — porosity, strut, material analysis
🔩 Nozzle Planner	Nozzle selection and coordination
🔧 Calibration	Guided multi-parameter calibration
🗺️ Toolpath Analyzer	G-code toolpath visualization
📋 Recipe Builder	Reproducible print recipe builder
📝 Protocol Library	Protocol management, tagging, comparison
⚖️ Protocol Compare	Side-by-side protocol comparison engine
🔮 Predictor	ML prediction of print outcomes

🧫 Cell Biology & Post-Print (7 tools)

Tool	Description
🧬 Cell Seeding	Seeding density and scaffold calculations
🧫 Maturation Tracker	Post-print tissue maturation tracking
📈 Growth Curve	Cell proliferation tracking
🔬 Passage Tracker	Cell passage tracking and lineage management
🧬 Western Blot	Western blot analysis and quantification
🧪 Flow Cytometry	Flow cytometry data analysis and gating
⚡ Electroporation Calculator	Electroporation protocol parameters

🏭 Lab Operations & Management (16 tools)

Tool	Description
💰 Cost Estimator	Per-print costs with materials, machine time, batch scaling
📊 Queue Manager	Print job scheduling and queue management
🏭 Batch Analytics	Batch processing queue and statistics
📊 Yield Analyzer	Print yield analysis and optimization
🌡️ Environment Monitor	Lab conditions — temp, humidity, CO₂, particulates
🛡️ Maintenance	Equipment maintenance scheduling and alerts
🚀 Fleet Commander	Multi-printer fleet management dashboard
🏭 Capacity Planner	Lab capacity planning and resource forecasting
📦 Sample Registry	Sample tracking and inventory management
📋 Sample Tracking	Sample tracking board with status
♻️ Waste Tracker	Material waste logging and trends
⏰ Expiry Watchdog	Reagent expiry tracking and alerting
🧹 Sterilization	Sterilization method selection and cycles
📅 Timeline Planner	Bioprint timeline planning and scheduling
📅 Smart Scheduler	Intelligent experiment scheduling
⏱️ Lab Timer	Multi-channel lab timer for protocol timing

📝 Compliance, Quality & Reporting (12 tools)

Tool	Description
📋 Print Report	Formatted, printable lab reports
📓 Print Logbook	Lab notebook — notes, tags, flags, search, export
📊 Print Profile	Individual print quality profiling with scoring
📈 Evolution Tracker	Print quality evolution over time
🔬 Failure Diagnostics	Root cause analysis and failure mode detection
🔧 Troubleshooter	Interactive bioprint troubleshooter
✅ GLP Compliance	Good Laboratory Practice compliance checks
🔗 Chain of Custody	Sample chain-of-custody tracking and audit trail
🔍 Data Integrity	Data integrity auditing and validation
🛡️ Safety Checklist	Lab safety checklist and compliance
🚨 Incident Report	Lab incident reporting and pattern analysis
⚠️ Risk Assessor	Experiment risk assessment and mitigation

🤖 Automation & Advanced (7 tools)

Tool	Description
🤖 Print Quality Autopilot	Autonomous print quality monitoring and adjustment
📝 Recommender	Parameter recommendation engine
🔄 Workflow Orchestrator	Lab workflow orchestration and automation
⚙️ Workflow Builder	Visual workflow builder for experiment pipelines
🔬 Experiment Replicator	Experiment replication planning and tracking
🧠 Knowledge Graph	Lab knowledge graph for experiment insights
⚠️ Early Warning	Contamination early warning and detection system

🔧 Utilities & Reference (12 tools)

Tool	Description
📋 Data Table	Searchable, sortable, filterable data browser with CSV export
🧫 Wellplate Analyzer	Performance breakdown by wellplate format
🧫 Plate Designer	Plate layout designer for experiment planning
🔄 Unit Converter	Bioprinting unit converter
📖 Glossary	Bioprinting terminology reference
🎬 Simulator	Print timeline simulator
🧬 Print Fingerprint	Print DNA fingerprinting for unique run identification
🎓 Training Tracker	Lab personnel training and certification tracking
🔍 Search Hub	Unified search and navigation across all tools
🔌 API Explorer	Interactive REST API documentation and testing
📚 Developer Guide	Setup, testing, and contributing reference
🏛️ Architecture	System architecture diagram

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📦 SDK — npm Package

The @sauravbhattacharya001/biobots package ships 80 factory functions for bioprinting computation — material calculations, rheology modeling, cell viability estimation, GCode analysis, and more.

npm install @sauravbhattacharya001/biobots

All modules are lazy-loaded — only the factories you call are loaded from disk, keeping require() startup fast.

Quick Examples

const biobots = require('@sauravbhattacharya001/biobots');

// Material usage estimation
const calc = biobots.createMaterialCalculator();
const usage = calc.calculateUsage({
  wellplate: 24, layerHeight: 0.2, layerNum: 10,
  materialKey: 'alginate', infillPercent: 80, wastePercent: 15
});
console.log(usage.totalVolumeMl, usage.estimatedCost);

// Rheology modeling (Power Law)
const rheo = biobots.createRheologyModeler();
const viscosity = rheo.powerLaw(100, { K: 50, n: 0.4 }); // η at γ̇ = 100 s⁻¹
const window = rheo.printabilityWindow({ K: 50, n: 0.4 });

// Cell viability estimation
const viability = biobots.createViabilityEstimator();
const result = viability.estimate({
  shearStress: 5.0,   // kPa
  duration: 120,       // seconds
  cellType: 'HeLa'
});
console.log(result.estimatedViability); // percentage

// GCode toolpath analysis
const gcode = biobots.createGCodeAnalyzer();
const analysis = gcode.analyze('G1 X10 Y20 Z0.2 E5 F1200\nG1 X30 Y20');
console.log(analysis.totalDistance, analysis.layerCount);

// Discover all available factories
console.log(biobots.listFactories()); // sorted array of 80 names
console.log(biobots.factoryCount);     // 80

Factory Categories

Category	Factories	Examples
Material Science	12	createMaterialCalculator, createBioinkMixer, createCompatibilityMatrix, createShelfLifeManager
Print Engineering	10	createGCodeAnalyzer, createScaffoldCalculator, createNozzleAdvisor, createRecipeBuilder
Cell Biology	8	createViabilityEstimator, createCellSeedingCalculator, createPassageTracker, createGrowthCurveAnalyzer
Rheology & Physics	5	createRheologyModeler, createCrosslinkAnalyzer, createElectroporationCalculator
Lab Operations	16	createLabInventoryManager, createSmartReorderAdvisor, createWasteTracker, createEnvironmentalMonitor, createSterilityAssurance
Quality & Analysis	12	createPrintQualityScorer, createYieldAnalyzer, createCapabilityAnalyzer, createDriftDetector
Data & Export	8	createDataExporter, createPrintSessionLogger, createSampleTracker, createDilutionCalculator
Automation	10	createProtocolGenerator, createJobEstimator, createMediaPrepCalculator, createCentrifugeCalculator

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📡 REST API

The ASP.NET Web API reads bioprinting data from a JSON dataset and exposes RESTful endpoints for statistical queries.

Endpoint Pattern

GET /api/prints/{metric}/{comparison}/{value}

Metrics

Metric	Type	Description
livePercent	double	Cell viability — % alive (live/dead imaging)
deadPercent	double	Cell mortality — % dead
elasticity	double	Structural rigidity (kPa)
cl_duration	int	Photocrosslinking duration (ms)
cl_intensity	int	Photocrosslinking light intensity (%)
extruder1 / extruder2	double	Extruder pressure at print time
layerHeight	double	Height per layer (mm)
layerNum	int	Total layer count
wellplate	int	Wellplate type
serial	int	BioBot 1 serial number

Comparisons & Aggregations

Comparison	Description
greater / lesser / equal	Count where metric matches condition

Pass Maximum, Minimum, or Average as the value for aggregation queries:

# Prints with >50% cell viability
GET /api/prints/livePercent/greater/50

# Maximum layer count
GET /api/prints/layerNum/greater/Maximum

# Average elasticity
GET /api/prints/elasticity/greater/Average

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🏗️ Architecture

BioBots/
├── docs/                      # 87 client-side analysis tools (GitHub Pages)
│   ├── shared/                # 80 SDK computation modules
│   ├── index.html             # Dashboard entry point
│   └── *.html                 # Individual tool pages
├── Try/                       # ASP.NET Web API backend
│   ├── Controllers/
│   │   └── PrintsController.cs    # REST API with 11 metric endpoints
│   ├── Models/
│   │   └── Print.cs               # Data models
│   └── Web.config
├── __tests__/                 # 146 Jest test files
├── tests/                     # Additional test modules
├── src/                       # Python analysis scripts
├── index.js                   # npm SDK entry — lazy-loaded factory manifest
├── index.d.ts                 # TypeScript type definitions
├── bioprint-data.json         # Sample dataset
└── BioBotsTool.sln            # .NET solution file

Key Design Decisions

• Thread-safe caching — Double-checked locking for concurrent request safety
• File-watch reload — Checks LastWriteTimeUtc on each request; re-parses only when changed
• Null-safe filtering — Records with missing nested objects are skipped with trace warnings
• Float equality — Epsilon-based comparison (1e-9) for IEEE 754 precision
• Lazy SDK loading — Factory modules loaded on first access, not at require() time

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🔧 Development

Prerequisites

• Node.js ≥ 18 (for SDK and tests)
• Visual Studio 2015+ with ASP.NET workload (for REST API)
• .NET Framework 4.x (for REST API)

Running Tests

npm install

# Full suite with coverage
npm test

# Watch mode
npx jest --watch

# Single file
npx jest __tests__/calculator.test.js

# Coverage thresholds (branches: 60%, functions/lines/statements: 70%)
npm run coverage:check

Running the REST API

1. Open BioBotsTool.sln in Visual Studio
2. Press F5 to start the development server
3. Navigate to http://localhost:{port}/index.html

Previewing Analysis Tools Locally

npx http-server docs -p 8000
# Open http://localhost:8000

Custom Data File

Add to Web.config:

<appSettings>
  <add key="DataFilePath" value="C:\path\to\your\bioprint-data.json" />
</appSettings>

The data file is watched — edits are picked up automatically.

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🚀 Deployment

Docker

docker pull ghcr.io/sauravbhattacharya001/biobots-tool:latest
docker run -p 8080:80 ghcr.io/sauravbhattacharya001/biobots-tool:latest

NuGet (GitHub Packages)

The BioBots.Models package provides data model classes for .NET projects:

dotnet nuget add source https://nuget.pkg.github.com/sauravbhattacharya001/index.json \
  --name github-biobots --username YOUR_GITHUB_USERNAME --password YOUR_GITHUB_PAT

dotnet add package BioBots.Models

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❓ Troubleshooting

Problem	Solution
API returns empty results	Verify bioprint-data.json exists and is valid JSON
Analysis tools show "No data"	Tools load bioprint-data.json via relative path — ensure the file is present
Tests fail with document is not defined	Run npm install — jsdom is required for DOM-dependent tests
Docker container won't start	Requires Windows containers (.NET Framework 4.x) — use --isolation=hyperv on Win 10/11
NuGet auth fails	GitHub Packages requires a PAT with read:packages scope

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🤝 Contributing

Contributions are welcome! See CONTRIBUTING.md for guidelines, ARCHITECTURE.md for system design, or the Developer Guide for setup instructions.

📄 License

MIT — Saurav Bhattacharya

👤 Author

Saurav Bhattacharya — @sauravbhattacharya001